Starting phenix.real_space_refine on Sat Mar 23 10:24:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v35_21028/03_2024/6v35_21028_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.342 sd= 1.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 248 5.16 5 C 23788 2.51 5 N 5828 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2097": "NH1" <-> "NH2" Residue "E ARG 2121": "NH1" <-> "NH2" Residue "E ARG 2163": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 735": "NH1" <-> "NH2" Residue "B ARG 972": "NH1" <-> "NH2" Residue "B PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 992": "OD1" <-> "OD2" Residue "B PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2097": "NH1" <-> "NH2" Residue "F ARG 2121": "NH1" <-> "NH2" Residue "F ARG 2163": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 707": "NH1" <-> "NH2" Residue "C ARG 735": "NH1" <-> "NH2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 992": "OD1" <-> "OD2" Residue "C PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2097": "NH1" <-> "NH2" Residue "G ARG 2121": "NH1" <-> "NH2" Residue "G ARG 2163": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ARG 735": "NH1" <-> "NH2" Residue "D ARG 972": "NH1" <-> "NH2" Residue "D PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 992": "OD1" <-> "OD2" Residue "D PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 2097": "NH1" <-> "NH2" Residue "H ARG 2121": "NH1" <-> "NH2" Residue "H ARG 2163": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36488 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "C" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "D" Number of atoms: 7287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7287 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 885} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Unusual residues: {'CLR': 1, 'PGW': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 69 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-1': 2, 'PGW:plan-2': 2, 'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Unusual residues: {'CLR': 1, 'PGW': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 78 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Unusual residues: {'CLR': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 69 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-1': 2, 'PGW:plan-2': 2, 'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Unusual residues: {'CLR': 1, 'PGW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 78 Unusual residues: {'CLR': 1, 'NAG': 2, 'PGW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 18.15, per 1000 atoms: 0.50 Number of scatterers: 36488 At special positions: 0 Unit cell: (159.9, 159.9, 165.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 12 15.00 O 6612 8.00 N 5828 7.00 C 23788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E2054 " - pdb=" SG CYS E2148 " distance=2.04 Simple disulfide: pdb=" SG CYS E2068 " - pdb=" SG CYS E2119 " distance=2.03 Simple disulfide: pdb=" SG CYS E2072 " - pdb=" SG CYS E2076 " distance=2.02 Simple disulfide: pdb=" SG CYS E2084 " - pdb=" SG CYS E2113 " distance=2.03 Simple disulfide: pdb=" SG CYS F2054 " - pdb=" SG CYS F2148 " distance=2.04 Simple disulfide: pdb=" SG CYS F2068 " - pdb=" SG CYS F2119 " distance=2.03 Simple disulfide: pdb=" SG CYS F2072 " - pdb=" SG CYS F2076 " distance=2.02 Simple disulfide: pdb=" SG CYS F2084 " - pdb=" SG CYS F2113 " distance=2.03 Simple disulfide: pdb=" SG CYS G2054 " - pdb=" SG CYS G2148 " distance=2.04 Simple disulfide: pdb=" SG CYS G2068 " - pdb=" SG CYS G2119 " distance=2.03 Simple disulfide: pdb=" SG CYS G2072 " - pdb=" SG CYS G2076 " distance=2.02 Simple disulfide: pdb=" SG CYS G2084 " - pdb=" SG CYS G2113 " distance=2.03 Simple disulfide: pdb=" SG CYS H2054 " - pdb=" SG CYS H2148 " distance=2.04 Simple disulfide: pdb=" SG CYS H2068 " - pdb=" SG CYS H2119 " distance=2.03 Simple disulfide: pdb=" SG CYS H2072 " - pdb=" SG CYS H2076 " distance=2.02 Simple disulfide: pdb=" SG CYS H2084 " - pdb=" SG CYS H2113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Links applied NAG-ASN " NAG E2303 " - " ASN E2053 " " NAG E2304 " - " ASN E2090 " " NAG F2304 " - " ASN F2053 " " NAG F2305 " - " ASN F2090 " " NAG G2303 " - " ASN G2053 " " NAG G2304 " - " ASN G2090 " " NAG H2304 " - " ASN H2053 " " NAG H2305 " - " ASN H2090 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.90 Conformation dependent library (CDL) restraints added in 6.5 seconds 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 28 sheets defined 43.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.48 Creating SS restraints... Processing helix chain 'A' and resid 22 through 46 removed outlier: 3.548A pdb=" N PHE A 25 " --> pdb=" O TRP A 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 35 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 37 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 43 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 46 " --> pdb=" O TRP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 4.314A pdb=" N TRP A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.339A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 4.031A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.643A pdb=" N TRP A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 208 through 223 removed outlier: 4.473A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 316 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.533A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.568A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.909A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.734A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 735 through 741 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 760 through 769 removed outlier: 4.301A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 removed outlier: 3.502A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.585A pdb=" N LEU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.740A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 890 " --> pdb=" O ASN A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 890' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 918 through 929 removed outlier: 3.732A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 947 through 956 removed outlier: 3.992A pdb=" N GLU A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 removed outlier: 3.537A pdb=" N ASN A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 4.224A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'E' and resid 2012 through 2035 removed outlier: 3.567A pdb=" N LEU E2032 " --> pdb=" O GLY E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2040 through 2046 removed outlier: 3.955A pdb=" N GLN E2045 " --> pdb=" O SER E2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP E2046 " --> pdb=" O PRO E2042 " (cutoff:3.500A) Processing helix chain 'E' and resid 2104 through 2109 removed outlier: 3.559A pdb=" N THR E2109 " --> pdb=" O HIS E2105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2123 through 2138 removed outlier: 3.620A pdb=" N TRP E2137 " --> pdb=" O TRP E2133 " (cutoff:3.500A) Processing helix chain 'E' and resid 2167 through 2199 removed outlier: 3.552A pdb=" N LEU E2170 " --> pdb=" O GLU E2167 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS E2172 " --> pdb=" O VAL E2169 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS E2173 " --> pdb=" O LEU E2170 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU E2175 " --> pdb=" O HIS E2172 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP E2176 " --> pdb=" O CYS E2173 " (cutoff:3.500A) Proline residue: E2177 - end of helix removed outlier: 3.801A pdb=" N VAL E2183 " --> pdb=" O THR E2180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E2187 " --> pdb=" O GLY E2184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E2189 " --> pdb=" O LEU E2186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E2190 " --> pdb=" O ILE E2187 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS E2193 " --> pdb=" O LEU E2190 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E2194 " --> pdb=" O THR E2191 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E2199 " --> pdb=" O SER E2196 " (cutoff:3.500A) Processing helix chain 'E' and resid 2201 through 2203 No H-bonds generated for 'chain 'E' and resid 2201 through 2203' Processing helix chain 'B' and resid 22 through 46 removed outlier: 3.546A pdb=" N PHE B 25 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY B 35 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 37 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 43 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 46 " --> pdb=" O TRP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 4.314A pdb=" N TRP B 100 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.339A pdb=" N SER B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 4.032A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.643A pdb=" N TRP B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.473A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 221 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 316 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.533A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.569A pdb=" N ALA B 467 " --> pdb=" O HIS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 Processing helix chain 'B' and resid 503 through 511 removed outlier: 3.908A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.734A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 735 through 741 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 760 through 769 removed outlier: 4.301A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 792 removed outlier: 3.502A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.586A pdb=" N LEU B 822 " --> pdb=" O LYS B 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 875 No H-bonds generated for 'chain 'B' and resid 873 through 875' Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.740A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 890 " --> pdb=" O ASN B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 890' Processing helix chain 'B' and resid 907 through 910 No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 918 through 929 removed outlier: 3.732A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 947 through 956 removed outlier: 3.993A pdb=" N GLU B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 removed outlier: 3.537A pdb=" N ASN B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 991 removed outlier: 4.224A pdb=" N ASP B 989 " --> pdb=" O PRO B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1006 Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'F' and resid 2012 through 2035 removed outlier: 3.567A pdb=" N LEU F2032 " --> pdb=" O GLY F2028 " (cutoff:3.500A) Processing helix chain 'F' and resid 2040 through 2046 removed outlier: 3.954A pdb=" N GLN F2045 " --> pdb=" O SER F2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F2046 " --> pdb=" O PRO F2042 " (cutoff:3.500A) Processing helix chain 'F' and resid 2104 through 2109 removed outlier: 3.559A pdb=" N THR F2109 " --> pdb=" O HIS F2105 " (cutoff:3.500A) Processing helix chain 'F' and resid 2123 through 2138 removed outlier: 3.619A pdb=" N TRP F2137 " --> pdb=" O TRP F2133 " (cutoff:3.500A) Processing helix chain 'F' and resid 2167 through 2199 removed outlier: 3.552A pdb=" N LEU F2170 " --> pdb=" O GLU F2167 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N HIS F2172 " --> pdb=" O VAL F2169 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS F2173 " --> pdb=" O LEU F2170 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F2175 " --> pdb=" O HIS F2172 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP F2176 " --> pdb=" O CYS F2173 " (cutoff:3.500A) Proline residue: F2177 - end of helix removed outlier: 3.802A pdb=" N VAL F2183 " --> pdb=" O THR F2180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE F2187 " --> pdb=" O GLY F2184 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL F2189 " --> pdb=" O LEU F2186 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F2190 " --> pdb=" O ILE F2187 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS F2193 " --> pdb=" O LEU F2190 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F2194 " --> pdb=" O THR F2191 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F2199 " --> pdb=" O SER F2196 " (cutoff:3.500A) Processing helix chain 'F' and resid 2201 through 2203 No H-bonds generated for 'chain 'F' and resid 2201 through 2203' Processing helix chain 'C' and resid 22 through 46 removed outlier: 3.547A pdb=" N PHE C 25 " --> pdb=" O TRP C 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 34 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 35 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 37 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 43 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 46 " --> pdb=" O TRP C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 4.313A pdb=" N TRP C 100 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 105 No H-bonds generated for 'chain 'C' and resid 102 through 105' Processing helix chain 'C' and resid 110 through 135 removed outlier: 4.338A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 removed outlier: 4.031A pdb=" N ASP C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.644A pdb=" N TRP C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 208 through 223 removed outlier: 4.473A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 221 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 258 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 316 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.533A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 433 through 450 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.569A pdb=" N ALA C 467 " --> pdb=" O HIS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 499 Processing helix chain 'C' and resid 503 through 511 removed outlier: 3.909A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 550 through 560 Processing helix chain 'C' and resid 602 through 608 removed outlier: 3.734A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 624 No H-bonds generated for 'chain 'C' and resid 622 through 624' Processing helix chain 'C' and resid 700 through 703 No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 735 through 741 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 760 through 769 removed outlier: 4.300A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 792 removed outlier: 3.502A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 818 through 828 removed outlier: 3.586A pdb=" N LEU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 875 No H-bonds generated for 'chain 'C' and resid 873 through 875' Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.740A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 890 " --> pdb=" O ASN C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 890' Processing helix chain 'C' and resid 907 through 910 No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 918 through 929 removed outlier: 3.732A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 926 " --> pdb=" O SER C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 947 through 956 removed outlier: 3.992A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 971 removed outlier: 3.537A pdb=" N ASN C 971 " --> pdb=" O GLN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 removed outlier: 4.223A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1006 Processing helix chain 'C' and resid 1018 through 1020 No H-bonds generated for 'chain 'C' and resid 1018 through 1020' Processing helix chain 'G' and resid 2012 through 2035 removed outlier: 3.566A pdb=" N LEU G2032 " --> pdb=" O GLY G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2040 through 2046 removed outlier: 3.955A pdb=" N GLN G2045 " --> pdb=" O SER G2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G2046 " --> pdb=" O PRO G2042 " (cutoff:3.500A) Processing helix chain 'G' and resid 2104 through 2109 removed outlier: 3.559A pdb=" N THR G2109 " --> pdb=" O HIS G2105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2123 through 2138 removed outlier: 3.620A pdb=" N TRP G2137 " --> pdb=" O TRP G2133 " (cutoff:3.500A) Processing helix chain 'G' and resid 2167 through 2199 removed outlier: 3.552A pdb=" N LEU G2170 " --> pdb=" O GLU G2167 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS G2172 " --> pdb=" O VAL G2169 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS G2173 " --> pdb=" O LEU G2170 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G2175 " --> pdb=" O HIS G2172 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP G2176 " --> pdb=" O CYS G2173 " (cutoff:3.500A) Proline residue: G2177 - end of helix removed outlier: 3.802A pdb=" N VAL G2183 " --> pdb=" O THR G2180 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE G2187 " --> pdb=" O GLY G2184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL G2189 " --> pdb=" O LEU G2186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G2190 " --> pdb=" O ILE G2187 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS G2193 " --> pdb=" O LEU G2190 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G2194 " --> pdb=" O THR G2191 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL G2199 " --> pdb=" O SER G2196 " (cutoff:3.500A) Processing helix chain 'G' and resid 2201 through 2203 No H-bonds generated for 'chain 'G' and resid 2201 through 2203' Processing helix chain 'D' and resid 22 through 46 removed outlier: 3.547A pdb=" N PHE D 25 " --> pdb=" O TRP D 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY D 35 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 37 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D 43 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 46 " --> pdb=" O TRP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 4.314A pdb=" N TRP D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'D' and resid 110 through 135 removed outlier: 4.338A pdb=" N SER D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 removed outlier: 4.031A pdb=" N ASP D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.643A pdb=" N TRP D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.473A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 221 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 316 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.532A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.568A pdb=" N ALA D 467 " --> pdb=" O HIS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 503 through 511 removed outlier: 3.909A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 602 through 608 removed outlier: 3.734A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 700 through 703 No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 735 through 741 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 760 through 769 removed outlier: 4.300A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 766 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 792 removed outlier: 3.502A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 818 through 828 removed outlier: 3.585A pdb=" N LEU D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 875 No H-bonds generated for 'chain 'D' and resid 873 through 875' Processing helix chain 'D' and resid 885 through 890 removed outlier: 3.740A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 890 " --> pdb=" O ASN D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 885 through 890' Processing helix chain 'D' and resid 907 through 910 No H-bonds generated for 'chain 'D' and resid 907 through 910' Processing helix chain 'D' and resid 918 through 929 removed outlier: 3.732A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 926 " --> pdb=" O SER D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 933 through 941 Processing helix chain 'D' and resid 947 through 956 removed outlier: 3.993A pdb=" N GLU D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 971 removed outlier: 3.538A pdb=" N ASN D 971 " --> pdb=" O GLN D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 991 removed outlier: 4.224A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1006 Processing helix chain 'D' and resid 1018 through 1020 No H-bonds generated for 'chain 'D' and resid 1018 through 1020' Processing helix chain 'H' and resid 2012 through 2035 removed outlier: 3.567A pdb=" N LEU H2032 " --> pdb=" O GLY H2028 " (cutoff:3.500A) Processing helix chain 'H' and resid 2040 through 2046 removed outlier: 3.955A pdb=" N GLN H2045 " --> pdb=" O SER H2041 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H2046 " --> pdb=" O PRO H2042 " (cutoff:3.500A) Processing helix chain 'H' and resid 2104 through 2109 removed outlier: 3.559A pdb=" N THR H2109 " --> pdb=" O HIS H2105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2123 through 2138 removed outlier: 3.619A pdb=" N TRP H2137 " --> pdb=" O TRP H2133 " (cutoff:3.500A) Processing helix chain 'H' and resid 2167 through 2199 removed outlier: 3.553A pdb=" N LEU H2170 " --> pdb=" O GLU H2167 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS H2172 " --> pdb=" O VAL H2169 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS H2173 " --> pdb=" O LEU H2170 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU H2175 " --> pdb=" O HIS H2172 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP H2176 " --> pdb=" O CYS H2173 " (cutoff:3.500A) Proline residue: H2177 - end of helix removed outlier: 3.801A pdb=" N VAL H2183 " --> pdb=" O THR H2180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE H2187 " --> pdb=" O GLY H2184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H2189 " --> pdb=" O LEU H2186 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H2190 " --> pdb=" O ILE H2187 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS H2193 " --> pdb=" O LEU H2190 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA H2194 " --> pdb=" O THR H2191 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H2199 " --> pdb=" O SER H2196 " (cutoff:3.500A) Processing helix chain 'H' and resid 2201 through 2203 No H-bonds generated for 'chain 'H' and resid 2201 through 2203' Processing sheet with id= A, first strand: chain 'A' and resid 482 through 485 removed outlier: 4.317A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.553A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 914 through 916 removed outlier: 7.109A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE A1049 " --> pdb=" O LEU A 980 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id= F, first strand: chain 'E' and resid 2050 through 2054 Processing sheet with id= G, first strand: chain 'E' and resid 2158 through 2160 removed outlier: 8.083A pdb=" N VAL E2159 " --> pdb=" O ARG E2097 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU E2099 " --> pdb=" O VAL E2159 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL E2087 " --> pdb=" O LEU E2100 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASN E2090 " --> pdb=" O VAL E2056 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL E2056 " --> pdb=" O ASN E2090 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 482 through 485 removed outlier: 4.316A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 535 through 540 removed outlier: 3.554A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 914 through 916 removed outlier: 7.109A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 978 through 981 removed outlier: 3.559A pdb=" N ILE B1049 " --> pdb=" O LEU B 980 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id= M, first strand: chain 'F' and resid 2050 through 2054 Processing sheet with id= N, first strand: chain 'F' and resid 2158 through 2160 removed outlier: 8.083A pdb=" N VAL F2159 " --> pdb=" O ARG F2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU F2099 " --> pdb=" O VAL F2159 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL F2087 " --> pdb=" O LEU F2100 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASN F2090 " --> pdb=" O VAL F2056 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL F2056 " --> pdb=" O ASN F2090 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 482 through 485 removed outlier: 4.316A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 535 through 540 removed outlier: 3.553A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 914 through 916 removed outlier: 7.109A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE C1049 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1014 through 1017 Processing sheet with id= T, first strand: chain 'G' and resid 2050 through 2054 Processing sheet with id= U, first strand: chain 'G' and resid 2158 through 2160 removed outlier: 8.084A pdb=" N VAL G2159 " --> pdb=" O ARG G2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU G2099 " --> pdb=" O VAL G2159 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL G2087 " --> pdb=" O LEU G2100 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN G2090 " --> pdb=" O VAL G2056 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL G2056 " --> pdb=" O ASN G2090 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 482 through 485 removed outlier: 4.317A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 535 through 540 removed outlier: 3.553A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 914 through 916 removed outlier: 7.110A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 978 through 981 removed outlier: 3.558A pdb=" N ILE D1049 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 1014 through 1017 Processing sheet with id= AA, first strand: chain 'H' and resid 2050 through 2054 Processing sheet with id= AB, first strand: chain 'H' and resid 2158 through 2160 removed outlier: 8.083A pdb=" N VAL H2159 " --> pdb=" O ARG H2097 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU H2099 " --> pdb=" O VAL H2159 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL H2087 " --> pdb=" O LEU H2100 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASN H2090 " --> pdb=" O VAL H2056 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL H2056 " --> pdb=" O ASN H2090 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3084 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.62 Time building geometry restraints manager: 15.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5780 1.30 - 1.43: 9993 1.43 - 1.56: 21021 1.56 - 1.69: 150 1.69 - 1.81: 356 Bond restraints: 37300 Sorted by residual: bond pdb=" C5 CLR H2306 " pdb=" C6 CLR H2306 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR E2305 " pdb=" C6 CLR E2305 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR G2305 " pdb=" C6 CLR G2305 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR F2306 " pdb=" C6 CLR F2306 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR C1107 " pdb=" C6 CLR C1107 " ideal model delta sigma weight residual 1.332 1.566 -0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 37295 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.48: 687 105.48 - 112.67: 19842 112.67 - 119.86: 13499 119.86 - 127.05: 16049 127.05 - 134.24: 427 Bond angle restraints: 50504 Sorted by residual: angle pdb=" O13 PGW B1104 " pdb=" P PGW B1104 " pdb=" O14 PGW B1104 " ideal model delta sigma weight residual 119.81 100.73 19.08 3.00e+00 1.11e-01 4.05e+01 angle pdb=" O13 PGW D1104 " pdb=" P PGW D1104 " pdb=" O14 PGW D1104 " ideal model delta sigma weight residual 119.81 100.73 19.08 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW A3001 " pdb=" P PGW A3001 " pdb=" O14 PGW A3001 " ideal model delta sigma weight residual 119.81 100.75 19.06 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW C1102 " pdb=" P PGW C1102 " pdb=" O14 PGW C1102 " ideal model delta sigma weight residual 119.81 100.75 19.06 3.00e+00 1.11e-01 4.04e+01 angle pdb=" O13 PGW D1101 " pdb=" P PGW D1101 " pdb=" O14 PGW D1101 " ideal model delta sigma weight residual 119.81 100.97 18.84 3.00e+00 1.11e-01 3.94e+01 ... (remaining 50499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.77: 21886 26.77 - 53.54: 566 53.54 - 80.32: 168 80.32 - 107.09: 56 107.09 - 133.86: 28 Dihedral angle restraints: 22704 sinusoidal: 9660 harmonic: 13044 Sorted by residual: dihedral pdb=" CB CYS F2054 " pdb=" SG CYS F2054 " pdb=" SG CYS F2148 " pdb=" CB CYS F2148 " ideal model delta sinusoidal sigma weight residual 93.00 178.44 -85.44 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS H2054 " pdb=" SG CYS H2054 " pdb=" SG CYS H2148 " pdb=" CB CYS H2148 " ideal model delta sinusoidal sigma weight residual 93.00 178.42 -85.42 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS E2054 " pdb=" SG CYS E2054 " pdb=" SG CYS E2148 " pdb=" CB CYS E2148 " ideal model delta sinusoidal sigma weight residual 93.00 178.41 -85.41 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 22701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 5362 0.135 - 0.270: 355 0.270 - 0.406: 26 0.406 - 0.541: 5 0.541 - 0.676: 8 Chirality restraints: 5756 Sorted by residual: chirality pdb=" C1 NAG F2304 " pdb=" ND2 ASN F2053 " pdb=" C2 NAG F2304 " pdb=" O5 NAG F2304 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG E2303 " pdb=" ND2 ASN E2053 " pdb=" C2 NAG E2303 " pdb=" O5 NAG E2303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG G2303 " pdb=" ND2 ASN G2053 " pdb=" C2 NAG G2303 " pdb=" O5 NAG G2303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 5753 not shown) Planarity restraints: 6248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1104 " 0.119 2.00e-02 2.50e+03 1.91e-01 3.64e+02 pdb=" C10 PGW B1104 " -0.242 2.00e-02 2.50e+03 pdb=" C8 PGW B1104 " -0.119 2.00e-02 2.50e+03 pdb=" C9 PGW B1104 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1102 " 0.119 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C10 PGW C1102 " -0.242 2.00e-02 2.50e+03 pdb=" C8 PGW C1102 " -0.119 2.00e-02 2.50e+03 pdb=" C9 PGW C1102 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A3001 " -0.119 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C10 PGW A3001 " 0.242 2.00e-02 2.50e+03 pdb=" C8 PGW A3001 " 0.119 2.00e-02 2.50e+03 pdb=" C9 PGW A3001 " -0.242 2.00e-02 2.50e+03 ... (remaining 6245 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10863 2.82 - 3.34: 34310 3.34 - 3.86: 61369 3.86 - 4.38: 70109 4.38 - 4.90: 117149 Nonbonded interactions: 293800 Sorted by model distance: nonbonded pdb=" O LEU D 214 " pdb=" OG SER D 240 " model vdw 2.296 2.440 nonbonded pdb=" O LEU A 214 " pdb=" OG SER A 240 " model vdw 2.296 2.440 nonbonded pdb=" O LEU B 214 " pdb=" OG SER B 240 " model vdw 2.297 2.440 nonbonded pdb=" O LEU C 214 " pdb=" OG SER C 240 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.302 2.440 ... (remaining 293795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1056 or resid 3003 or (resid 3005 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) selection = (chain 'B' and (resid 19 through 1056 or resid 1103 or (resid 1105 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) selection = (chain 'C' and (resid 19 through 1056 or (resid 1103 and (name C1 or name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 1105 and (name C20 or name C21 or name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27)))) selection = (chain 'D' and (resid 19 through 1056 or resid 1103 or (resid 1105 and (name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27)))) } ncs_group { reference = (chain 'E' and (resid 2008 through 2205 or resid 2301 through 2302 or resid 2304 \ )) selection = (chain 'F' and (resid 2008 through 2205 or (resid 2301 and (name C1 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 2302 and (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 2304)) selection = (chain 'G' and (resid 2008 through 2205 or resid 2301 through 2302 or resid 2304 \ )) selection = (chain 'H' and (resid 2008 through 2205 or (resid 2301 and (name C1 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 2302 and (nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 2304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.150 Check model and map are aligned: 0.470 Set scattering table: 0.350 Process input model: 92.820 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 37300 Z= 0.722 Angle : 1.233 19.081 50504 Z= 0.681 Chirality : 0.075 0.676 5756 Planarity : 0.008 0.191 6240 Dihedral : 14.970 133.861 14200 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.81 % Allowed : 4.27 % Favored : 94.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 4408 helix: -2.06 (0.09), residues: 1936 sheet: -1.71 (0.21), residues: 576 loop : -2.04 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 246 HIS 0.011 0.002 HIS D 254 PHE 0.033 0.003 PHE C 164 TYR 0.026 0.002 TYR C1015 ARG 0.011 0.001 ARG B1031 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 847 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.9439 (tp) cc_final: 0.9143 (tp) REVERT: A 30 MET cc_start: 0.8565 (ttm) cc_final: 0.8314 (mmm) REVERT: A 214 LEU cc_start: 0.9273 (mt) cc_final: 0.8949 (mp) REVERT: A 276 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 282 MET cc_start: 0.8784 (tpp) cc_final: 0.8555 (tpp) REVERT: A 356 VAL cc_start: 0.9738 (t) cc_final: 0.9499 (t) REVERT: A 374 GLU cc_start: 0.7848 (tt0) cc_final: 0.7390 (tp30) REVERT: A 460 MET cc_start: 0.9049 (mmm) cc_final: 0.8683 (mmm) REVERT: A 878 ILE cc_start: 0.9086 (pt) cc_final: 0.8882 (mt) REVERT: E 2015 ASP cc_start: 0.8841 (t70) cc_final: 0.8527 (t0) REVERT: E 2016 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8340 (tptt) REVERT: E 2046 ASP cc_start: 0.8773 (t70) cc_final: 0.8384 (t0) REVERT: E 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8666 (mmm160) REVERT: E 2115 TYR cc_start: 0.9182 (t80) cc_final: 0.8757 (t80) REVERT: E 2163 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: E 2168 ILE cc_start: 0.8433 (tt) cc_final: 0.8179 (tt) REVERT: B 214 LEU cc_start: 0.9191 (mt) cc_final: 0.8926 (mp) REVERT: B 276 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7881 (mm-30) REVERT: B 282 MET cc_start: 0.8706 (tpp) cc_final: 0.8458 (tpp) REVERT: B 356 VAL cc_start: 0.9728 (t) cc_final: 0.9494 (t) REVERT: B 374 GLU cc_start: 0.7803 (tt0) cc_final: 0.7507 (tp30) REVERT: B 460 MET cc_start: 0.9078 (mmm) cc_final: 0.8775 (mmm) REVERT: F 2015 ASP cc_start: 0.8949 (t70) cc_final: 0.8729 (t0) REVERT: F 2016 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8348 (tptt) REVERT: F 2046 ASP cc_start: 0.8701 (t70) cc_final: 0.8188 (t0) REVERT: F 2077 ARG cc_start: 0.8948 (mmt90) cc_final: 0.8676 (mmm160) REVERT: F 2115 TYR cc_start: 0.9192 (t80) cc_final: 0.8758 (t80) REVERT: F 2163 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7698 (mtt-85) REVERT: F 2168 ILE cc_start: 0.8484 (tt) cc_final: 0.8181 (mt) REVERT: F 2191 THR cc_start: 0.9092 (m) cc_final: 0.8828 (m) REVERT: C 26 LEU cc_start: 0.9438 (tp) cc_final: 0.9142 (tp) REVERT: C 30 MET cc_start: 0.8579 (ttm) cc_final: 0.8319 (mmm) REVERT: C 214 LEU cc_start: 0.9273 (mt) cc_final: 0.8951 (mp) REVERT: C 276 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 282 MET cc_start: 0.8785 (tpp) cc_final: 0.8554 (tpp) REVERT: C 356 VAL cc_start: 0.9731 (t) cc_final: 0.9458 (p) REVERT: C 374 GLU cc_start: 0.7775 (tt0) cc_final: 0.7464 (tp30) REVERT: C 460 MET cc_start: 0.9042 (mmm) cc_final: 0.8669 (mmm) REVERT: G 2015 ASP cc_start: 0.8841 (t70) cc_final: 0.8521 (t0) REVERT: G 2016 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8339 (tptt) REVERT: G 2046 ASP cc_start: 0.8775 (t70) cc_final: 0.8388 (t0) REVERT: G 2077 ARG cc_start: 0.8921 (mmt90) cc_final: 0.8663 (mmm160) REVERT: G 2115 TYR cc_start: 0.9177 (t80) cc_final: 0.8759 (t80) REVERT: G 2155 ARG cc_start: 0.8153 (mpp-170) cc_final: 0.7673 (mtt90) REVERT: G 2163 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7753 (mtt-85) REVERT: D 26 LEU cc_start: 0.9463 (tp) cc_final: 0.9261 (tp) REVERT: D 214 LEU cc_start: 0.9181 (mt) cc_final: 0.8937 (mp) REVERT: D 276 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7799 (mm-30) REVERT: D 282 MET cc_start: 0.8689 (tpp) cc_final: 0.8424 (tpp) REVERT: D 356 VAL cc_start: 0.9741 (t) cc_final: 0.9537 (t) REVERT: D 362 ASP cc_start: 0.8148 (t0) cc_final: 0.7709 (t0) REVERT: D 374 GLU cc_start: 0.7977 (tt0) cc_final: 0.7538 (tp30) REVERT: D 460 MET cc_start: 0.9055 (mmm) cc_final: 0.8722 (mmm) REVERT: D 513 MET cc_start: 0.7499 (mmm) cc_final: 0.7285 (mmm) REVERT: D 1030 LYS cc_start: 0.9137 (mttt) cc_final: 0.8670 (mtmt) REVERT: H 2015 ASP cc_start: 0.8944 (t70) cc_final: 0.8727 (t0) REVERT: H 2016 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8327 (tptt) REVERT: H 2046 ASP cc_start: 0.8752 (t70) cc_final: 0.8136 (t0) REVERT: H 2077 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8617 (mmm160) REVERT: H 2115 TYR cc_start: 0.9250 (t80) cc_final: 0.8742 (t80) REVERT: H 2163 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7560 (mtp180) REVERT: H 2168 ILE cc_start: 0.8557 (tt) cc_final: 0.8287 (mt) REVERT: H 2191 THR cc_start: 0.9082 (m) cc_final: 0.8824 (m) outliers start: 32 outliers final: 10 residues processed: 879 average time/residue: 0.4963 time to fit residues: 696.1642 Evaluate side-chains 469 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 459 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 4.9990 chunk 333 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 399 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 440 ASN A 465 ASN A 471 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 809 ASN E2106 GLN E2124 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 440 ASN B 471 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 809 ASN F2106 GLN F2124 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 HIS C 440 ASN C 465 ASN C 471 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 ASN C 809 ASN G2106 GLN G2124 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 HIS D 440 ASN D 465 ASN D 468 HIS D 471 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 809 ASN H2124 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 37300 Z= 0.243 Angle : 0.641 11.625 50504 Z= 0.320 Chirality : 0.044 0.395 5756 Planarity : 0.004 0.048 6240 Dihedral : 14.036 133.335 5996 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.62 % Allowed : 9.68 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 4408 helix: -0.81 (0.11), residues: 1976 sheet: -1.57 (0.19), residues: 640 loop : -1.49 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E2176 HIS 0.008 0.001 HIS B 254 PHE 0.025 0.002 PHE G2033 TYR 0.014 0.001 TYR G2008 ARG 0.006 0.001 ARG E2155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 509 time to evaluate : 3.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9365 (tp) cc_final: 0.9063 (pp) REVERT: A 162 LEU cc_start: 0.9448 (mt) cc_final: 0.9081 (pp) REVERT: A 214 LEU cc_start: 0.9291 (mt) cc_final: 0.9077 (mp) REVERT: A 285 MET cc_start: 0.8404 (mmm) cc_final: 0.8152 (mmm) REVERT: A 306 PHE cc_start: 0.8707 (t80) cc_final: 0.8399 (t80) REVERT: A 356 VAL cc_start: 0.9740 (t) cc_final: 0.9523 (t) REVERT: A 362 ASP cc_start: 0.7983 (t0) cc_final: 0.7364 (t0) REVERT: A 569 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 609 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8354 (t80) REVERT: A 1053 MET cc_start: 0.8515 (mtp) cc_final: 0.8215 (mtm) REVERT: E 2015 ASP cc_start: 0.8997 (t70) cc_final: 0.8720 (t0) REVERT: E 2016 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8581 (tptt) REVERT: E 2046 ASP cc_start: 0.8742 (t70) cc_final: 0.8532 (t70) REVERT: E 2077 ARG cc_start: 0.8936 (mmt90) cc_final: 0.8646 (mmm160) REVERT: E 2163 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7763 (mtp180) REVERT: B 118 LEU cc_start: 0.9288 (tp) cc_final: 0.8991 (pp) REVERT: B 282 MET cc_start: 0.8887 (tpp) cc_final: 0.8684 (tpp) REVERT: B 285 MET cc_start: 0.8246 (mmm) cc_final: 0.7917 (mmm) REVERT: B 356 VAL cc_start: 0.9740 (t) cc_final: 0.9536 (t) REVERT: B 362 ASP cc_start: 0.8031 (t0) cc_final: 0.7401 (t0) REVERT: B 900 ASP cc_start: 0.8760 (p0) cc_final: 0.8519 (p0) REVERT: B 1053 MET cc_start: 0.8516 (mtp) cc_final: 0.8235 (mtm) REVERT: F 2015 ASP cc_start: 0.8953 (t70) cc_final: 0.8702 (t0) REVERT: F 2016 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8434 (tptt) REVERT: F 2046 ASP cc_start: 0.8702 (t70) cc_final: 0.8471 (t70) REVERT: F 2077 ARG cc_start: 0.9008 (mmt90) cc_final: 0.8638 (mmm160) REVERT: F 2163 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7713 (mtp180) REVERT: C 118 LEU cc_start: 0.9362 (tp) cc_final: 0.9062 (pp) REVERT: C 162 LEU cc_start: 0.9450 (mt) cc_final: 0.9080 (pp) REVERT: C 214 LEU cc_start: 0.9291 (mt) cc_final: 0.9075 (mp) REVERT: C 285 MET cc_start: 0.8413 (mmm) cc_final: 0.8173 (mmm) REVERT: C 306 PHE cc_start: 0.8707 (t80) cc_final: 0.8397 (t80) REVERT: C 356 VAL cc_start: 0.9739 (t) cc_final: 0.9530 (p) REVERT: C 362 ASP cc_start: 0.8021 (t0) cc_final: 0.7402 (t0) REVERT: C 569 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7607 (mm-30) REVERT: G 2015 ASP cc_start: 0.8994 (t70) cc_final: 0.8716 (t0) REVERT: G 2016 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8546 (tptt) REVERT: G 2046 ASP cc_start: 0.8783 (t70) cc_final: 0.8556 (t70) REVERT: G 2077 ARG cc_start: 0.9015 (mmt90) cc_final: 0.8643 (mmm160) REVERT: G 2163 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7819 (mtt-85) REVERT: D 118 LEU cc_start: 0.9304 (tp) cc_final: 0.8911 (pp) REVERT: D 285 MET cc_start: 0.8400 (mmm) cc_final: 0.8131 (mmm) REVERT: D 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7965 (t80) REVERT: D 356 VAL cc_start: 0.9756 (t) cc_final: 0.9544 (t) REVERT: D 362 ASP cc_start: 0.8086 (t0) cc_final: 0.7520 (t0) REVERT: D 705 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (pp) REVERT: D 900 ASP cc_start: 0.8653 (p0) cc_final: 0.8424 (p0) REVERT: H 2015 ASP cc_start: 0.8948 (t70) cc_final: 0.8674 (t0) REVERT: H 2016 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8257 (tptt) REVERT: H 2046 ASP cc_start: 0.8718 (t70) cc_final: 0.8422 (t70) REVERT: H 2077 ARG cc_start: 0.8972 (mmt90) cc_final: 0.8600 (mmm160) REVERT: H 2115 TYR cc_start: 0.9309 (t80) cc_final: 0.8853 (t80) REVERT: H 2163 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7605 (mtp180) outliers start: 103 outliers final: 41 residues processed: 583 average time/residue: 0.4523 time to fit residues: 445.1351 Evaluate side-chains 467 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 424 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2187 ILE Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 814 SER Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 400 optimal weight: 0.8980 chunk 432 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 358 ASN A 468 HIS ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 465 ASN B 468 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37300 Z= 0.215 Angle : 0.577 10.952 50504 Z= 0.286 Chirality : 0.042 0.350 5756 Planarity : 0.004 0.051 6240 Dihedral : 12.411 148.960 5987 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.64 % Allowed : 10.44 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4408 helix: -0.17 (0.12), residues: 1968 sheet: -1.37 (0.21), residues: 588 loop : -1.32 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G2176 HIS 0.007 0.001 HIS B 254 PHE 0.026 0.001 PHE H2033 TYR 0.015 0.001 TYR F2008 ARG 0.004 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 459 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9348 (tp) cc_final: 0.9072 (pp) REVERT: A 162 LEU cc_start: 0.9395 (mt) cc_final: 0.9018 (pp) REVERT: A 214 LEU cc_start: 0.9298 (mt) cc_final: 0.9051 (mt) REVERT: A 285 MET cc_start: 0.8377 (mmm) cc_final: 0.8120 (mmm) REVERT: A 303 PHE cc_start: 0.8159 (t80) cc_final: 0.7896 (t80) REVERT: A 362 ASP cc_start: 0.8004 (t0) cc_final: 0.7468 (t0) REVERT: A 569 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 715 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8149 (pp) REVERT: A 799 MET cc_start: 0.8336 (ttm) cc_final: 0.8096 (ttm) REVERT: A 830 MET cc_start: 0.8279 (mtp) cc_final: 0.7962 (ttm) REVERT: A 1009 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8259 (ttm) REVERT: A 1053 MET cc_start: 0.8586 (mtp) cc_final: 0.8370 (mtm) REVERT: E 2015 ASP cc_start: 0.8949 (t70) cc_final: 0.8696 (t0) REVERT: E 2016 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8641 (tptt) REVERT: E 2046 ASP cc_start: 0.8740 (t70) cc_final: 0.8534 (t70) REVERT: E 2077 ARG cc_start: 0.8939 (mmt90) cc_final: 0.8560 (mmm160) REVERT: E 2163 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7368 (mmm160) REVERT: B 118 LEU cc_start: 0.9302 (tp) cc_final: 0.8982 (pp) REVERT: B 162 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8978 (pp) REVERT: B 362 ASP cc_start: 0.8014 (t0) cc_final: 0.7487 (t0) REVERT: B 715 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8069 (pp) REVERT: F 2015 ASP cc_start: 0.8949 (t70) cc_final: 0.8671 (t0) REVERT: F 2016 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8545 (tptt) REVERT: F 2046 ASP cc_start: 0.8715 (t70) cc_final: 0.8472 (t70) REVERT: F 2077 ARG cc_start: 0.8991 (mmt90) cc_final: 0.8568 (mmm160) REVERT: F 2155 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.7028 (mpt-90) REVERT: F 2163 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7341 (mmm160) REVERT: C 30 MET cc_start: 0.9092 (mmm) cc_final: 0.8867 (mmt) REVERT: C 118 LEU cc_start: 0.9346 (tp) cc_final: 0.9070 (pp) REVERT: C 162 LEU cc_start: 0.9395 (mt) cc_final: 0.9016 (pp) REVERT: C 214 LEU cc_start: 0.9283 (mt) cc_final: 0.9056 (mt) REVERT: C 276 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8359 (mm-30) REVERT: C 285 MET cc_start: 0.8387 (mmm) cc_final: 0.8127 (mmm) REVERT: C 303 PHE cc_start: 0.8160 (t80) cc_final: 0.7899 (t80) REVERT: C 362 ASP cc_start: 0.8014 (t0) cc_final: 0.7487 (t0) REVERT: C 569 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7427 (mm-30) REVERT: C 715 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8081 (pp) REVERT: C 799 MET cc_start: 0.8354 (ttm) cc_final: 0.8118 (ttm) REVERT: G 2015 ASP cc_start: 0.8944 (t70) cc_final: 0.8690 (t0) REVERT: G 2016 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8667 (tptt) REVERT: G 2046 ASP cc_start: 0.8745 (t70) cc_final: 0.8520 (t70) REVERT: G 2077 ARG cc_start: 0.8992 (mmt90) cc_final: 0.8561 (mmm160) REVERT: G 2163 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7336 (mmm160) REVERT: D 30 MET cc_start: 0.8940 (mmm) cc_final: 0.8737 (mmt) REVERT: D 118 LEU cc_start: 0.9285 (tp) cc_final: 0.8895 (pp) REVERT: D 162 LEU cc_start: 0.9427 (mm) cc_final: 0.9041 (pp) REVERT: D 285 MET cc_start: 0.8383 (mmm) cc_final: 0.7856 (mmm) REVERT: D 303 PHE cc_start: 0.8145 (t80) cc_final: 0.7861 (t80) REVERT: D 307 PHE cc_start: 0.8011 (t80) cc_final: 0.7640 (t80) REVERT: D 362 ASP cc_start: 0.8077 (t0) cc_final: 0.7845 (t0) REVERT: D 715 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8578 (pp) REVERT: D 830 MET cc_start: 0.8211 (mtp) cc_final: 0.7887 (ttm) REVERT: D 878 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8859 (mp) REVERT: D 900 ASP cc_start: 0.8766 (p0) cc_final: 0.8527 (p0) REVERT: H 2015 ASP cc_start: 0.8943 (t70) cc_final: 0.8642 (t0) REVERT: H 2016 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8345 (tptt) REVERT: H 2023 PHE cc_start: 0.9174 (t80) cc_final: 0.8929 (t80) REVERT: H 2046 ASP cc_start: 0.8715 (t70) cc_final: 0.8448 (t70) REVERT: H 2077 ARG cc_start: 0.8964 (mmt90) cc_final: 0.8583 (mmm160) REVERT: H 2115 TYR cc_start: 0.9299 (t80) cc_final: 0.9099 (t80) REVERT: H 2163 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7686 (mtp180) outliers start: 104 outliers final: 58 residues processed: 519 average time/residue: 0.4530 time to fit residues: 392.9442 Evaluate side-chains 464 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 399 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain E residue 2103 ASP Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2103 ASP Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 814 SER Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 814 SER Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 949 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 216 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 GLN C 143 ASN C 216 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN D 143 ASN D 216 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN D 932 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37300 Z= 0.266 Angle : 0.578 10.601 50504 Z= 0.289 Chirality : 0.042 0.331 5756 Planarity : 0.003 0.049 6240 Dihedral : 11.460 154.421 5979 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.00 % Allowed : 11.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4408 helix: 0.20 (0.12), residues: 1944 sheet: -1.39 (0.21), residues: 600 loop : -1.01 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G2176 HIS 0.008 0.001 HIS B 254 PHE 0.022 0.002 PHE G2033 TYR 0.008 0.001 TYR G2008 ARG 0.003 0.001 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 429 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9355 (tp) cc_final: 0.9102 (pp) REVERT: A 162 LEU cc_start: 0.9378 (mt) cc_final: 0.9011 (pp) REVERT: A 214 LEU cc_start: 0.9321 (mt) cc_final: 0.9067 (mt) REVERT: A 273 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9079 (p) REVERT: A 285 MET cc_start: 0.8413 (mmm) cc_final: 0.8126 (mmm) REVERT: A 303 PHE cc_start: 0.8307 (t80) cc_final: 0.8057 (t80) REVERT: A 306 PHE cc_start: 0.8661 (t80) cc_final: 0.8398 (t80) REVERT: A 321 GLU cc_start: 0.8219 (mp0) cc_final: 0.7950 (mp0) REVERT: A 362 ASP cc_start: 0.8120 (t0) cc_final: 0.7870 (t0) REVERT: A 569 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 715 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8509 (pp) REVERT: A 799 MET cc_start: 0.8389 (ttm) cc_final: 0.8112 (ttm) REVERT: A 830 MET cc_start: 0.8211 (mtp) cc_final: 0.7986 (ttm) REVERT: A 1009 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: E 2015 ASP cc_start: 0.9021 (t70) cc_final: 0.8794 (t0) REVERT: E 2016 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8658 (tptt) REVERT: E 2046 ASP cc_start: 0.8677 (t70) cc_final: 0.8428 (t70) REVERT: E 2077 ARG cc_start: 0.8989 (mmt90) cc_final: 0.8528 (mmm160) REVERT: E 2163 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7402 (mmm160) REVERT: B 118 LEU cc_start: 0.9278 (tp) cc_final: 0.9012 (pp) REVERT: B 273 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9080 (p) REVERT: B 285 MET cc_start: 0.8434 (mmm) cc_final: 0.8233 (mmm) REVERT: B 306 PHE cc_start: 0.8699 (t80) cc_final: 0.8463 (t80) REVERT: B 321 GLU cc_start: 0.8212 (mp0) cc_final: 0.7895 (mp0) REVERT: B 362 ASP cc_start: 0.8094 (t0) cc_final: 0.7876 (t0) REVERT: B 477 TRP cc_start: 0.7459 (OUTLIER) cc_final: 0.7193 (p90) REVERT: B 575 ARG cc_start: 0.6534 (mpp-170) cc_final: 0.6242 (mpp-170) REVERT: B 715 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8238 (pp) REVERT: F 2015 ASP cc_start: 0.9045 (t70) cc_final: 0.8747 (t0) REVERT: F 2016 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8517 (tptt) REVERT: F 2046 ASP cc_start: 0.8683 (t70) cc_final: 0.8480 (t70) REVERT: F 2077 ARG cc_start: 0.8982 (mmt90) cc_final: 0.8544 (mmm160) REVERT: F 2163 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7440 (mmm160) REVERT: C 118 LEU cc_start: 0.9351 (tp) cc_final: 0.9099 (pp) REVERT: C 162 LEU cc_start: 0.9380 (mt) cc_final: 0.9009 (pp) REVERT: C 214 LEU cc_start: 0.9373 (mt) cc_final: 0.9088 (mt) REVERT: C 273 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.9054 (p) REVERT: C 285 MET cc_start: 0.8417 (mmm) cc_final: 0.8152 (mmm) REVERT: C 303 PHE cc_start: 0.8283 (t80) cc_final: 0.8060 (t80) REVERT: C 306 PHE cc_start: 0.8651 (t80) cc_final: 0.8380 (t80) REVERT: C 321 GLU cc_start: 0.8219 (mp0) cc_final: 0.7951 (mp0) REVERT: C 362 ASP cc_start: 0.8151 (t0) cc_final: 0.7922 (t0) REVERT: C 569 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 627 LYS cc_start: 0.7932 (tptt) cc_final: 0.7702 (tppt) REVERT: C 715 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8497 (pp) REVERT: C 799 MET cc_start: 0.8391 (ttm) cc_final: 0.8121 (ttm) REVERT: G 2015 ASP cc_start: 0.9015 (t70) cc_final: 0.8790 (t0) REVERT: G 2016 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8657 (tptt) REVERT: G 2046 ASP cc_start: 0.8697 (t70) cc_final: 0.8431 (t70) REVERT: G 2077 ARG cc_start: 0.8992 (mmt90) cc_final: 0.8551 (mmm160) REVERT: G 2163 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7300 (mmm160) REVERT: D 118 LEU cc_start: 0.9286 (tp) cc_final: 0.8954 (pp) REVERT: D 154 MET cc_start: 0.8037 (mtm) cc_final: 0.7755 (mtm) REVERT: D 162 LEU cc_start: 0.9414 (mm) cc_final: 0.9196 (mm) REVERT: D 285 MET cc_start: 0.8420 (mmm) cc_final: 0.8130 (mmm) REVERT: D 303 PHE cc_start: 0.8267 (t80) cc_final: 0.8036 (t80) REVERT: D 362 ASP cc_start: 0.8132 (t0) cc_final: 0.7915 (t0) REVERT: D 442 MET cc_start: 0.8777 (tpp) cc_final: 0.8566 (tpp) REVERT: D 715 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (pp) REVERT: D 878 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8918 (mp) REVERT: H 2015 ASP cc_start: 0.9021 (t70) cc_final: 0.8714 (t0) REVERT: H 2016 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8452 (tptt) REVERT: H 2023 PHE cc_start: 0.9207 (t80) cc_final: 0.8954 (t80) REVERT: H 2077 ARG cc_start: 0.8975 (mmt90) cc_final: 0.8535 (mmm160) REVERT: H 2115 TYR cc_start: 0.9327 (t80) cc_final: 0.9089 (t80) REVERT: H 2163 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.7776 (mtp180) REVERT: H 2176 TRP cc_start: 0.8546 (m100) cc_final: 0.8289 (m100) REVERT: H 2190 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8868 (mp) outliers start: 118 outliers final: 72 residues processed: 496 average time/residue: 0.4607 time to fit residues: 385.2565 Evaluate side-chains 479 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 396 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain E residue 2103 ASP Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 477 TRP Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain F residue 2103 ASP Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2103 ASP Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain H residue 2103 ASP Chi-restraints excluded: chain H residue 2190 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 316 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 362 optimal weight: 0.0870 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 381 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 358 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 358 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37300 Z= 0.138 Angle : 0.517 10.230 50504 Z= 0.256 Chirality : 0.040 0.309 5756 Planarity : 0.003 0.046 6240 Dihedral : 10.229 128.868 5979 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4408 helix: 0.41 (0.12), residues: 1984 sheet: -1.36 (0.20), residues: 612 loop : -1.10 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E2176 HIS 0.006 0.001 HIS A 254 PHE 0.009 0.001 PHE C 164 TYR 0.007 0.001 TYR A 904 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 441 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9302 (tp) cc_final: 0.9056 (pp) REVERT: A 214 LEU cc_start: 0.9268 (mt) cc_final: 0.9020 (mt) REVERT: A 285 MET cc_start: 0.8422 (mmm) cc_final: 0.7997 (mmm) REVERT: A 303 PHE cc_start: 0.7987 (t80) cc_final: 0.7713 (t80) REVERT: A 569 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 691 MET cc_start: 0.8246 (mmt) cc_final: 0.8021 (mmt) REVERT: A 715 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8152 (pp) REVERT: A 799 MET cc_start: 0.8273 (ttm) cc_final: 0.7966 (ttm) REVERT: E 2015 ASP cc_start: 0.9007 (t70) cc_final: 0.8729 (t0) REVERT: E 2016 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8625 (tptt) REVERT: E 2046 ASP cc_start: 0.8676 (t70) cc_final: 0.8086 (t0) REVERT: E 2077 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8563 (mmm160) REVERT: E 2163 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7221 (mmm160) REVERT: B 21 MET cc_start: 0.8451 (mmm) cc_final: 0.7904 (mmm) REVERT: B 118 LEU cc_start: 0.9251 (tp) cc_final: 0.9039 (pp) REVERT: B 162 LEU cc_start: 0.9408 (mm) cc_final: 0.8969 (pp) REVERT: B 575 ARG cc_start: 0.6420 (mpp-170) cc_final: 0.6108 (mpp-170) REVERT: B 715 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8075 (pp) REVERT: F 2015 ASP cc_start: 0.8962 (t70) cc_final: 0.8633 (t0) REVERT: F 2016 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8514 (tptt) REVERT: F 2046 ASP cc_start: 0.8632 (t70) cc_final: 0.8245 (t70) REVERT: F 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8552 (mmm160) REVERT: F 2163 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7345 (mmm160) REVERT: C 118 LEU cc_start: 0.9299 (tp) cc_final: 0.9054 (pp) REVERT: C 214 LEU cc_start: 0.9296 (mt) cc_final: 0.9034 (mt) REVERT: C 285 MET cc_start: 0.8470 (mmm) cc_final: 0.8049 (mmm) REVERT: C 307 PHE cc_start: 0.8006 (t80) cc_final: 0.7685 (t80) REVERT: C 321 GLU cc_start: 0.8187 (mp0) cc_final: 0.7768 (mp0) REVERT: C 569 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7341 (mm-30) REVERT: C 691 MET cc_start: 0.8287 (mmt) cc_final: 0.8065 (mmt) REVERT: C 715 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8127 (pp) REVERT: C 799 MET cc_start: 0.8280 (ttm) cc_final: 0.7960 (ttm) REVERT: G 2015 ASP cc_start: 0.8994 (t70) cc_final: 0.8705 (t0) REVERT: G 2016 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8626 (tptt) REVERT: G 2046 ASP cc_start: 0.8701 (t70) cc_final: 0.8142 (t0) REVERT: G 2077 ARG cc_start: 0.8925 (mmt90) cc_final: 0.8559 (mmm160) REVERT: G 2163 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7198 (mmm160) REVERT: D 21 MET cc_start: 0.8366 (mmm) cc_final: 0.7869 (mmm) REVERT: D 118 LEU cc_start: 0.9251 (tp) cc_final: 0.8960 (pp) REVERT: D 162 LEU cc_start: 0.9416 (mm) cc_final: 0.9162 (mm) REVERT: D 273 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9040 (p) REVERT: D 285 MET cc_start: 0.8431 (mmm) cc_final: 0.7976 (mmm) REVERT: D 303 PHE cc_start: 0.7999 (t80) cc_final: 0.7704 (t80) REVERT: D 306 PHE cc_start: 0.8593 (t80) cc_final: 0.8382 (t80) REVERT: D 307 PHE cc_start: 0.7991 (t80) cc_final: 0.7680 (t80) REVERT: D 442 MET cc_start: 0.8878 (tpp) cc_final: 0.8603 (tpp) REVERT: D 627 LYS cc_start: 0.7647 (tptt) cc_final: 0.7328 (tppt) REVERT: D 715 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8304 (pp) REVERT: D 878 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8863 (mp) REVERT: H 2015 ASP cc_start: 0.8982 (t70) cc_final: 0.8646 (t0) REVERT: H 2016 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8410 (tptt) REVERT: H 2023 PHE cc_start: 0.9173 (t80) cc_final: 0.8925 (t80) REVERT: H 2046 ASP cc_start: 0.8520 (t70) cc_final: 0.8084 (t0) REVERT: H 2077 ARG cc_start: 0.8874 (mmt90) cc_final: 0.8512 (mmm160) outliers start: 82 outliers final: 52 residues processed: 491 average time/residue: 0.4518 time to fit residues: 374.0254 Evaluate side-chains 450 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 392 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 9.9990 chunk 383 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 425 optimal weight: 5.9990 chunk 353 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37300 Z= 0.188 Angle : 0.537 9.655 50504 Z= 0.263 Chirality : 0.040 0.300 5756 Planarity : 0.003 0.048 6240 Dihedral : 9.961 121.934 5979 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.36 % Allowed : 14.05 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4408 helix: 0.63 (0.12), residues: 1952 sheet: -1.46 (0.20), residues: 644 loop : -0.81 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E2176 HIS 0.006 0.001 HIS B 254 PHE 0.022 0.001 PHE F2033 TYR 0.010 0.001 TYR H2008 ARG 0.004 0.000 ARG B 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 398 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8538 (mmm) cc_final: 0.7926 (mmm) REVERT: A 118 LEU cc_start: 0.9286 (tp) cc_final: 0.9050 (pp) REVERT: A 162 LEU cc_start: 0.9367 (mt) cc_final: 0.9009 (pp) REVERT: A 214 LEU cc_start: 0.9330 (mt) cc_final: 0.9087 (mt) REVERT: A 273 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 276 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 460 MET cc_start: 0.8077 (mtp) cc_final: 0.7744 (ttt) REVERT: A 691 MET cc_start: 0.8274 (mmt) cc_final: 0.7987 (mmt) REVERT: A 715 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8220 (pp) REVERT: A 799 MET cc_start: 0.8300 (ttm) cc_final: 0.8010 (ttm) REVERT: E 2015 ASP cc_start: 0.9005 (t70) cc_final: 0.8713 (t0) REVERT: E 2016 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8621 (tptt) REVERT: E 2023 PHE cc_start: 0.9126 (t80) cc_final: 0.8911 (t80) REVERT: E 2046 ASP cc_start: 0.8691 (t70) cc_final: 0.8136 (t0) REVERT: E 2077 ARG cc_start: 0.8903 (mmt90) cc_final: 0.8502 (mmm160) REVERT: E 2163 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7246 (mmm160) REVERT: B 21 MET cc_start: 0.8544 (mmm) cc_final: 0.8074 (mmm) REVERT: B 118 LEU cc_start: 0.9233 (tp) cc_final: 0.8990 (pp) REVERT: B 162 LEU cc_start: 0.9434 (mm) cc_final: 0.9213 (mm) REVERT: B 273 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9085 (p) REVERT: B 282 MET cc_start: 0.8753 (tpp) cc_final: 0.8525 (tpp) REVERT: B 285 MET cc_start: 0.8459 (mmm) cc_final: 0.8256 (mmm) REVERT: B 575 ARG cc_start: 0.6560 (mpp-170) cc_final: 0.6280 (mpp-170) REVERT: B 691 MET cc_start: 0.8253 (mmt) cc_final: 0.8044 (mmt) REVERT: B 715 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8127 (pp) REVERT: F 2015 ASP cc_start: 0.8983 (t70) cc_final: 0.8636 (t0) REVERT: F 2016 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8502 (tptt) REVERT: F 2046 ASP cc_start: 0.8653 (t70) cc_final: 0.8297 (t70) REVERT: F 2077 ARG cc_start: 0.8896 (mmt90) cc_final: 0.8545 (mmm160) REVERT: F 2163 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7264 (mmm160) REVERT: C 21 MET cc_start: 0.8497 (mmm) cc_final: 0.7897 (mmm) REVERT: C 118 LEU cc_start: 0.9311 (tp) cc_final: 0.9060 (pp) REVERT: C 162 LEU cc_start: 0.9367 (mt) cc_final: 0.9008 (pp) REVERT: C 214 LEU cc_start: 0.9357 (mt) cc_final: 0.9093 (mt) REVERT: C 273 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9049 (p) REVERT: C 285 MET cc_start: 0.8485 (mmm) cc_final: 0.8235 (mmm) REVERT: C 460 MET cc_start: 0.8036 (mtp) cc_final: 0.7724 (ttt) REVERT: C 569 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7188 (mm-30) REVERT: C 575 ARG cc_start: 0.6481 (mpp-170) cc_final: 0.6116 (mpp-170) REVERT: C 627 LYS cc_start: 0.7567 (tptt) cc_final: 0.7289 (tppt) REVERT: C 691 MET cc_start: 0.8302 (mmt) cc_final: 0.8085 (mmt) REVERT: C 715 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8188 (pp) REVERT: C 799 MET cc_start: 0.8310 (ttm) cc_final: 0.8022 (ttm) REVERT: G 2015 ASP cc_start: 0.9006 (t70) cc_final: 0.8713 (t0) REVERT: G 2016 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8621 (tptt) REVERT: G 2023 PHE cc_start: 0.9135 (t80) cc_final: 0.8927 (t80) REVERT: G 2046 ASP cc_start: 0.8720 (t70) cc_final: 0.8127 (t0) REVERT: G 2077 ARG cc_start: 0.8912 (mmt90) cc_final: 0.8523 (mmm160) REVERT: G 2163 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7208 (mmm160) REVERT: D 21 MET cc_start: 0.8520 (mmm) cc_final: 0.8013 (mmm) REVERT: D 118 LEU cc_start: 0.9238 (tp) cc_final: 0.8934 (pp) REVERT: D 154 MET cc_start: 0.7663 (mtm) cc_final: 0.7461 (mtm) REVERT: D 162 LEU cc_start: 0.9415 (mm) cc_final: 0.9174 (mm) REVERT: D 273 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8950 (p) REVERT: D 285 MET cc_start: 0.8461 (mmm) cc_final: 0.8176 (mmm) REVERT: D 306 PHE cc_start: 0.8626 (t80) cc_final: 0.8393 (t80) REVERT: D 386 GLU cc_start: 0.7946 (tp30) cc_final: 0.7732 (tp30) REVERT: D 442 MET cc_start: 0.8805 (tpp) cc_final: 0.8412 (tpp) REVERT: D 627 LYS cc_start: 0.7766 (tptt) cc_final: 0.7407 (tppt) REVERT: D 691 MET cc_start: 0.8169 (mmt) cc_final: 0.7928 (mmt) REVERT: D 715 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8556 (pp) REVERT: H 2015 ASP cc_start: 0.8980 (t70) cc_final: 0.8629 (t0) REVERT: H 2016 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8449 (tptt) REVERT: H 2023 PHE cc_start: 0.9142 (t80) cc_final: 0.8928 (t80) REVERT: H 2077 ARG cc_start: 0.8869 (mmt90) cc_final: 0.8503 (mmm160) outliers start: 93 outliers final: 54 residues processed: 461 average time/residue: 0.4255 time to fit residues: 331.9804 Evaluate side-chains 440 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 378 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 358 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 424 optimal weight: 0.4980 chunk 265 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37300 Z= 0.211 Angle : 0.547 9.560 50504 Z= 0.268 Chirality : 0.041 0.294 5756 Planarity : 0.003 0.049 6240 Dihedral : 9.720 122.039 5979 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.64 % Allowed : 14.00 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4408 helix: 0.70 (0.12), residues: 1952 sheet: -1.47 (0.20), residues: 644 loop : -0.73 (0.16), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E2176 HIS 0.007 0.001 HIS C 254 PHE 0.025 0.001 PHE E2033 TYR 0.012 0.001 TYR H2008 ARG 0.003 0.000 ARG B 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 389 time to evaluate : 4.813 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9289 (tp) cc_final: 0.9049 (pp) REVERT: A 214 LEU cc_start: 0.9328 (mt) cc_final: 0.9014 (mt) REVERT: A 273 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 276 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 303 PHE cc_start: 0.8288 (t80) cc_final: 0.8006 (t80) REVERT: A 306 PHE cc_start: 0.8590 (t80) cc_final: 0.8375 (t80) REVERT: A 460 MET cc_start: 0.8113 (mtp) cc_final: 0.7908 (ttt) REVERT: A 691 MET cc_start: 0.8274 (mmt) cc_final: 0.7999 (mmt) REVERT: A 715 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (pp) REVERT: A 799 MET cc_start: 0.8327 (ttm) cc_final: 0.8033 (ttm) REVERT: E 2015 ASP cc_start: 0.9010 (t70) cc_final: 0.8708 (t0) REVERT: E 2016 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8632 (tptt) REVERT: E 2023 PHE cc_start: 0.9162 (t80) cc_final: 0.8948 (t80) REVERT: E 2046 ASP cc_start: 0.8698 (t70) cc_final: 0.8145 (t0) REVERT: E 2077 ARG cc_start: 0.8939 (mmt90) cc_final: 0.8484 (mmm160) REVERT: E 2163 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7215 (mmm160) REVERT: B 118 LEU cc_start: 0.9240 (tp) cc_final: 0.8998 (pp) REVERT: B 162 LEU cc_start: 0.9423 (mm) cc_final: 0.8993 (pp) REVERT: B 206 LEU cc_start: 0.9329 (mt) cc_final: 0.9124 (mp) REVERT: B 273 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9078 (p) REVERT: B 460 MET cc_start: 0.8082 (mtp) cc_final: 0.7810 (ttm) REVERT: B 627 LYS cc_start: 0.7429 (tptt) cc_final: 0.7022 (tppt) REVERT: B 691 MET cc_start: 0.8285 (mmt) cc_final: 0.8053 (mmt) REVERT: B 715 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8367 (pp) REVERT: F 2015 ASP cc_start: 0.8985 (t70) cc_final: 0.8631 (t0) REVERT: F 2016 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8496 (tptt) REVERT: F 2046 ASP cc_start: 0.8664 (t70) cc_final: 0.8328 (t70) REVERT: F 2077 ARG cc_start: 0.8896 (mmt90) cc_final: 0.8513 (mmm160) REVERT: F 2163 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7283 (mmm160) REVERT: F 2176 TRP cc_start: 0.8166 (m100) cc_final: 0.7966 (m-10) REVERT: C 21 MET cc_start: 0.8456 (mmm) cc_final: 0.8014 (mmm) REVERT: C 118 LEU cc_start: 0.9318 (tp) cc_final: 0.9060 (pp) REVERT: C 192 PRO cc_start: 0.9155 (Cg_exo) cc_final: 0.8890 (Cg_endo) REVERT: C 214 LEU cc_start: 0.9366 (mt) cc_final: 0.9104 (mt) REVERT: C 273 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9009 (p) REVERT: C 285 MET cc_start: 0.8475 (mmm) cc_final: 0.8218 (mmm) REVERT: C 306 PHE cc_start: 0.8703 (t80) cc_final: 0.8483 (t80) REVERT: C 569 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 575 ARG cc_start: 0.6510 (mpp-170) cc_final: 0.6222 (mpp-170) REVERT: C 691 MET cc_start: 0.8285 (mmt) cc_final: 0.8021 (mmt) REVERT: C 715 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (pp) REVERT: G 2015 ASP cc_start: 0.9010 (t70) cc_final: 0.8710 (t0) REVERT: G 2016 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8598 (tptt) REVERT: G 2023 PHE cc_start: 0.9157 (t80) cc_final: 0.8946 (t80) REVERT: G 2046 ASP cc_start: 0.8725 (t70) cc_final: 0.8142 (t0) REVERT: G 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8507 (mmm160) REVERT: G 2163 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.6911 (mmm160) REVERT: D 30 MET cc_start: 0.9239 (mmp) cc_final: 0.8904 (mmp) REVERT: D 118 LEU cc_start: 0.9248 (tp) cc_final: 0.8938 (pp) REVERT: D 154 MET cc_start: 0.7702 (mtm) cc_final: 0.7480 (mtm) REVERT: D 162 LEU cc_start: 0.9415 (mm) cc_final: 0.9128 (mm) REVERT: D 273 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9033 (p) REVERT: D 285 MET cc_start: 0.8466 (mmm) cc_final: 0.8165 (mmm) REVERT: D 303 PHE cc_start: 0.8272 (t80) cc_final: 0.8015 (t80) REVERT: D 386 GLU cc_start: 0.8030 (tp30) cc_final: 0.7795 (tp30) REVERT: D 442 MET cc_start: 0.8751 (tpp) cc_final: 0.8410 (tpp) REVERT: D 627 LYS cc_start: 0.7591 (tptt) cc_final: 0.7311 (tppt) REVERT: D 691 MET cc_start: 0.8227 (mmt) cc_final: 0.7978 (mmt) REVERT: D 715 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8567 (pp) REVERT: H 2015 ASP cc_start: 0.8986 (t70) cc_final: 0.8629 (t0) REVERT: H 2016 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8448 (tptt) REVERT: H 2023 PHE cc_start: 0.9159 (t80) cc_final: 0.8958 (t80) REVERT: H 2077 ARG cc_start: 0.8856 (mmt90) cc_final: 0.8543 (mmm160) REVERT: H 2176 TRP cc_start: 0.8169 (m100) cc_final: 0.7943 (m-10) outliers start: 104 outliers final: 74 residues processed: 456 average time/residue: 0.4450 time to fit residues: 343.6244 Evaluate side-chains 463 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 381 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2103 ASP Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2162 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 ASN F2162 HIS ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2162 HIS ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37300 Z= 0.233 Angle : 0.565 9.369 50504 Z= 0.277 Chirality : 0.041 0.292 5756 Planarity : 0.003 0.049 6240 Dihedral : 9.537 123.229 5979 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.54 % Allowed : 14.38 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4408 helix: 0.71 (0.12), residues: 1964 sheet: -1.45 (0.20), residues: 644 loop : -0.70 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP G2176 HIS 0.007 0.001 HIS B 254 PHE 0.028 0.001 PHE G2033 TYR 0.011 0.001 TYR H2008 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 395 time to evaluate : 4.013 Fit side-chains REVERT: A 21 MET cc_start: 0.8360 (mmm) cc_final: 0.7833 (mmm) REVERT: A 118 LEU cc_start: 0.9299 (tp) cc_final: 0.9053 (pp) REVERT: A 214 LEU cc_start: 0.9351 (mt) cc_final: 0.9053 (mt) REVERT: A 273 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 276 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 303 PHE cc_start: 0.8309 (t80) cc_final: 0.7999 (t80) REVERT: A 306 PHE cc_start: 0.8675 (t80) cc_final: 0.8471 (t80) REVERT: A 627 LYS cc_start: 0.7613 (tptt) cc_final: 0.7258 (tppt) REVERT: A 691 MET cc_start: 0.8290 (mmt) cc_final: 0.7994 (mmt) REVERT: A 715 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8584 (pp) REVERT: E 2015 ASP cc_start: 0.9004 (t70) cc_final: 0.8701 (t0) REVERT: E 2016 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8598 (tptt) REVERT: E 2023 PHE cc_start: 0.9159 (t80) cc_final: 0.8952 (t80) REVERT: E 2046 ASP cc_start: 0.8695 (t70) cc_final: 0.8356 (t70) REVERT: E 2077 ARG cc_start: 0.8929 (mmt90) cc_final: 0.8480 (mmm160) REVERT: E 2163 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.6960 (mmm160) REVERT: B 21 MET cc_start: 0.8427 (mmm) cc_final: 0.6866 (mtt) REVERT: B 46 LEU cc_start: 0.9045 (mt) cc_final: 0.8828 (pp) REVERT: B 118 LEU cc_start: 0.9291 (tp) cc_final: 0.8977 (pp) REVERT: B 162 LEU cc_start: 0.9367 (mm) cc_final: 0.8921 (pp) REVERT: B 206 LEU cc_start: 0.9357 (mt) cc_final: 0.9138 (mp) REVERT: B 273 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 460 MET cc_start: 0.8203 (mtp) cc_final: 0.7913 (ttm) REVERT: B 627 LYS cc_start: 0.7487 (tptt) cc_final: 0.7066 (tppt) REVERT: B 691 MET cc_start: 0.8289 (mmt) cc_final: 0.8038 (mmt) REVERT: B 715 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (pp) REVERT: F 2015 ASP cc_start: 0.8995 (t70) cc_final: 0.8632 (t0) REVERT: F 2016 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8459 (tptt) REVERT: F 2023 PHE cc_start: 0.9141 (t80) cc_final: 0.8912 (t80) REVERT: F 2046 ASP cc_start: 0.8643 (t70) cc_final: 0.8315 (t70) REVERT: F 2077 ARG cc_start: 0.8879 (mmt90) cc_final: 0.8468 (mmm160) REVERT: F 2163 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7219 (mmm160) REVERT: F 2176 TRP cc_start: 0.8288 (m100) cc_final: 0.7956 (m100) REVERT: C 30 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8917 (mmm) REVERT: C 46 LEU cc_start: 0.9080 (mt) cc_final: 0.8873 (pp) REVERT: C 118 LEU cc_start: 0.9325 (tp) cc_final: 0.9065 (pp) REVERT: C 192 PRO cc_start: 0.9153 (Cg_exo) cc_final: 0.8901 (Cg_endo) REVERT: C 214 LEU cc_start: 0.9368 (mt) cc_final: 0.9057 (mt) REVERT: C 273 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9078 (p) REVERT: C 285 MET cc_start: 0.8473 (mmm) cc_final: 0.8199 (mmm) REVERT: C 306 PHE cc_start: 0.8729 (t80) cc_final: 0.8521 (t80) REVERT: C 321 GLU cc_start: 0.8261 (mp0) cc_final: 0.7895 (mp0) REVERT: C 569 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7234 (mm-30) REVERT: C 575 ARG cc_start: 0.6539 (mpp-170) cc_final: 0.6245 (mpp-170) REVERT: C 691 MET cc_start: 0.8372 (mmt) cc_final: 0.8089 (mmt) REVERT: C 715 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8562 (pp) REVERT: G 2015 ASP cc_start: 0.9003 (t70) cc_final: 0.8701 (t0) REVERT: G 2016 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8593 (tptt) REVERT: G 2046 ASP cc_start: 0.8726 (t70) cc_final: 0.8480 (t70) REVERT: G 2077 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8500 (mmm160) REVERT: G 2163 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7538 (mtp180) REVERT: D 21 MET cc_start: 0.8392 (mmm) cc_final: 0.6829 (mtt) REVERT: D 46 LEU cc_start: 0.9042 (mt) cc_final: 0.8821 (pp) REVERT: D 118 LEU cc_start: 0.9280 (tp) cc_final: 0.8963 (pp) REVERT: D 154 MET cc_start: 0.7746 (mtm) cc_final: 0.7538 (mtm) REVERT: D 162 LEU cc_start: 0.9400 (mm) cc_final: 0.8974 (pp) REVERT: D 221 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9281 (tt) REVERT: D 273 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9060 (p) REVERT: D 285 MET cc_start: 0.8456 (mmm) cc_final: 0.8164 (mmm) REVERT: D 303 PHE cc_start: 0.8285 (t80) cc_final: 0.8024 (t80) REVERT: D 442 MET cc_start: 0.8734 (tpp) cc_final: 0.8414 (tpp) REVERT: D 460 MET cc_start: 0.8069 (mtp) cc_final: 0.7836 (ttt) REVERT: D 626 LYS cc_start: 0.8614 (mmmt) cc_final: 0.7939 (mmmt) REVERT: D 627 LYS cc_start: 0.7724 (tptt) cc_final: 0.7398 (tppt) REVERT: D 691 MET cc_start: 0.8294 (mmt) cc_final: 0.8031 (mmt) REVERT: D 715 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8564 (pp) REVERT: D 878 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8954 (mp) REVERT: H 2015 ASP cc_start: 0.8991 (t70) cc_final: 0.8632 (t0) REVERT: H 2016 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8453 (tptt) REVERT: H 2077 ARG cc_start: 0.8837 (mmt90) cc_final: 0.8550 (mmm160) REVERT: H 2176 TRP cc_start: 0.8258 (m100) cc_final: 0.7874 (m100) outliers start: 100 outliers final: 73 residues processed: 460 average time/residue: 0.4437 time to fit residues: 345.0052 Evaluate side-chains 473 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 389 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2103 ASP Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2103 ASP Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2103 ASP Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2103 ASP Chi-restraints excluded: chain H residue 2180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 7.9990 chunk 406 optimal weight: 0.5980 chunk 370 optimal weight: 2.9990 chunk 395 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 373 optimal weight: 0.7980 chunk 393 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2101 HIS ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 37300 Z= 0.147 Angle : 0.541 9.645 50504 Z= 0.263 Chirality : 0.040 0.285 5756 Planarity : 0.003 0.048 6240 Dihedral : 8.919 127.160 5979 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.03 % Allowed : 15.29 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4408 helix: 0.86 (0.13), residues: 1920 sheet: -1.38 (0.20), residues: 640 loop : -0.68 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP G2176 HIS 0.006 0.001 HIS B 254 PHE 0.038 0.001 PHE H2023 TYR 0.012 0.001 TYR F2008 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 424 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8394 (mmm) cc_final: 0.7930 (mmm) REVERT: A 48 TYR cc_start: 0.8718 (m-10) cc_final: 0.8476 (m-80) REVERT: A 118 LEU cc_start: 0.9267 (tp) cc_final: 0.9038 (pp) REVERT: A 161 LEU cc_start: 0.9645 (tp) cc_final: 0.9324 (pp) REVERT: A 214 LEU cc_start: 0.9336 (mt) cc_final: 0.9041 (mt) REVERT: A 273 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9095 (p) REVERT: A 303 PHE cc_start: 0.8234 (t80) cc_final: 0.7900 (t80) REVERT: A 306 PHE cc_start: 0.8624 (t80) cc_final: 0.8390 (t80) REVERT: A 626 LYS cc_start: 0.8622 (mmmt) cc_final: 0.7987 (mmmt) REVERT: A 627 LYS cc_start: 0.7595 (tptt) cc_final: 0.7256 (tppt) REVERT: A 691 MET cc_start: 0.8233 (mmt) cc_final: 0.7898 (mmt) REVERT: A 715 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pp) REVERT: E 2015 ASP cc_start: 0.8985 (t70) cc_final: 0.8673 (t0) REVERT: E 2016 LYS cc_start: 0.9079 (ttmt) cc_final: 0.8629 (tptt) REVERT: E 2077 ARG cc_start: 0.8920 (mmt90) cc_final: 0.8454 (mmm160) REVERT: B 21 MET cc_start: 0.8388 (mmm) cc_final: 0.7948 (mmm) REVERT: B 46 LEU cc_start: 0.9030 (mt) cc_final: 0.8823 (pp) REVERT: B 118 LEU cc_start: 0.9230 (tp) cc_final: 0.8999 (pp) REVERT: B 159 PHE cc_start: 0.9032 (t80) cc_final: 0.8740 (t80) REVERT: B 162 LEU cc_start: 0.9386 (mm) cc_final: 0.8956 (pp) REVERT: B 273 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8865 (p) REVERT: B 460 MET cc_start: 0.8044 (mtp) cc_final: 0.7783 (ttm) REVERT: B 626 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8052 (mmmt) REVERT: B 627 LYS cc_start: 0.7513 (tptt) cc_final: 0.7160 (tppt) REVERT: B 691 MET cc_start: 0.8257 (mmt) cc_final: 0.7991 (mmt) REVERT: B 715 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8151 (pp) REVERT: F 2015 ASP cc_start: 0.8931 (t70) cc_final: 0.8604 (t0) REVERT: F 2016 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8561 (tptt) REVERT: F 2023 PHE cc_start: 0.9140 (t80) cc_final: 0.8931 (t80) REVERT: F 2046 ASP cc_start: 0.8635 (t70) cc_final: 0.8328 (t70) REVERT: F 2077 ARG cc_start: 0.8854 (mmt90) cc_final: 0.8474 (mmm160) REVERT: F 2163 ARG cc_start: 0.7685 (mtt-85) cc_final: 0.7353 (mtp180) REVERT: C 21 MET cc_start: 0.8306 (mmm) cc_final: 0.7776 (mmm) REVERT: C 46 LEU cc_start: 0.9056 (mt) cc_final: 0.8849 (pp) REVERT: C 118 LEU cc_start: 0.9277 (tp) cc_final: 0.9041 (pp) REVERT: C 161 LEU cc_start: 0.9646 (tp) cc_final: 0.9326 (pp) REVERT: C 192 PRO cc_start: 0.9152 (Cg_exo) cc_final: 0.8883 (Cg_endo) REVERT: C 214 LEU cc_start: 0.9354 (mt) cc_final: 0.9087 (mt) REVERT: C 285 MET cc_start: 0.8457 (mmm) cc_final: 0.8193 (mmm) REVERT: C 321 GLU cc_start: 0.8223 (mp0) cc_final: 0.7877 (tt0) REVERT: C 459 GLN cc_start: 0.8615 (mt0) cc_final: 0.8245 (mt0) REVERT: C 460 MET cc_start: 0.7866 (mtp) cc_final: 0.7625 (ttt) REVERT: C 569 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7030 (mm-30) REVERT: C 626 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8083 (mmmt) REVERT: C 627 LYS cc_start: 0.7509 (tptt) cc_final: 0.7217 (tppt) REVERT: C 691 MET cc_start: 0.8223 (mmt) cc_final: 0.7982 (mmt) REVERT: C 715 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (pp) REVERT: C 1009 MET cc_start: 0.7469 (ttm) cc_final: 0.6701 (tpp) REVERT: G 2015 ASP cc_start: 0.8988 (t70) cc_final: 0.8679 (t0) REVERT: G 2016 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8626 (tptt) REVERT: G 2046 ASP cc_start: 0.8696 (t70) cc_final: 0.8454 (t70) REVERT: G 2077 ARG cc_start: 0.8884 (mmt90) cc_final: 0.8510 (mmm160) REVERT: D 21 MET cc_start: 0.8351 (mmm) cc_final: 0.7898 (mmm) REVERT: D 46 LEU cc_start: 0.9050 (mt) cc_final: 0.8830 (pp) REVERT: D 118 LEU cc_start: 0.9243 (tp) cc_final: 0.8941 (pp) REVERT: D 159 PHE cc_start: 0.9008 (t80) cc_final: 0.8553 (t80) REVERT: D 162 LEU cc_start: 0.9379 (mm) cc_final: 0.8952 (pp) REVERT: D 273 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9063 (p) REVERT: D 285 MET cc_start: 0.8461 (mmm) cc_final: 0.8173 (mmm) REVERT: D 303 PHE cc_start: 0.8201 (t80) cc_final: 0.7941 (t80) REVERT: D 386 GLU cc_start: 0.8025 (tp30) cc_final: 0.7786 (tp30) REVERT: D 442 MET cc_start: 0.8685 (tpp) cc_final: 0.8459 (tpp) REVERT: D 460 MET cc_start: 0.7944 (mtp) cc_final: 0.7701 (ttt) REVERT: D 626 LYS cc_start: 0.8564 (mmmt) cc_final: 0.7947 (mmmt) REVERT: D 627 LYS cc_start: 0.7709 (tptt) cc_final: 0.7354 (tppt) REVERT: D 691 MET cc_start: 0.8375 (mmt) cc_final: 0.8124 (mmt) REVERT: D 715 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (pp) REVERT: D 819 GLU cc_start: 0.7612 (mp0) cc_final: 0.7411 (mp0) REVERT: D 878 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8918 (mp) REVERT: H 2015 ASP cc_start: 0.8930 (t70) cc_final: 0.8612 (t0) REVERT: H 2016 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8397 (tptt) REVERT: H 2077 ARG cc_start: 0.8804 (mmt90) cc_final: 0.8567 (mmm160) outliers start: 80 outliers final: 64 residues processed: 473 average time/residue: 0.4464 time to fit residues: 354.6541 Evaluate side-chains 471 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 399 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 745 ASN Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 0.9990 chunk 417 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 198 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 438 optimal weight: 5.9990 chunk 403 optimal weight: 8.9990 chunk 349 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37300 Z= 0.152 Angle : 0.548 9.461 50504 Z= 0.266 Chirality : 0.040 0.282 5756 Planarity : 0.003 0.057 6240 Dihedral : 8.905 128.316 5979 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.01 % Allowed : 15.47 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4408 helix: 0.88 (0.13), residues: 1920 sheet: -1.34 (0.20), residues: 640 loop : -0.65 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP H2176 HIS 0.007 0.001 HIS B 254 PHE 0.039 0.001 PHE H2023 TYR 0.009 0.001 TYR B 48 ARG 0.005 0.000 ARG D 976 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 400 time to evaluate : 4.313 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8405 (mmm) cc_final: 0.7965 (mmm) REVERT: A 48 TYR cc_start: 0.8763 (m-10) cc_final: 0.8528 (m-80) REVERT: A 118 LEU cc_start: 0.9260 (tp) cc_final: 0.9041 (pp) REVERT: A 214 LEU cc_start: 0.9332 (mt) cc_final: 0.9035 (mt) REVERT: A 273 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.9003 (p) REVERT: A 303 PHE cc_start: 0.8032 (t80) cc_final: 0.7753 (t80) REVERT: A 306 PHE cc_start: 0.8611 (t80) cc_final: 0.8388 (t80) REVERT: A 626 LYS cc_start: 0.8528 (mmmt) cc_final: 0.7848 (mmmt) REVERT: A 627 LYS cc_start: 0.7585 (tptt) cc_final: 0.7224 (tppt) REVERT: A 691 MET cc_start: 0.8239 (mmt) cc_final: 0.8032 (mmm) REVERT: A 715 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (pp) REVERT: E 2015 ASP cc_start: 0.8978 (t70) cc_final: 0.8663 (t0) REVERT: E 2016 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8565 (tptt) REVERT: E 2077 ARG cc_start: 0.8918 (mmt90) cc_final: 0.8456 (mmm160) REVERT: B 21 MET cc_start: 0.8391 (mmm) cc_final: 0.7976 (mmm) REVERT: B 46 LEU cc_start: 0.9033 (mt) cc_final: 0.8827 (pp) REVERT: B 118 LEU cc_start: 0.9250 (tp) cc_final: 0.8967 (pp) REVERT: B 159 PHE cc_start: 0.9047 (t80) cc_final: 0.8748 (t80) REVERT: B 162 LEU cc_start: 0.9386 (mm) cc_final: 0.9016 (pp) REVERT: B 460 MET cc_start: 0.7997 (mtp) cc_final: 0.7742 (ttm) REVERT: B 626 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7942 (mmmt) REVERT: B 627 LYS cc_start: 0.7511 (tptt) cc_final: 0.7145 (tppt) REVERT: B 691 MET cc_start: 0.8251 (mmt) cc_final: 0.7919 (mmt) REVERT: B 715 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8109 (pp) REVERT: F 2015 ASP cc_start: 0.8922 (t70) cc_final: 0.8597 (t0) REVERT: F 2016 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8551 (tptt) REVERT: F 2046 ASP cc_start: 0.8620 (t70) cc_final: 0.8309 (t70) REVERT: F 2077 ARG cc_start: 0.8850 (mmt90) cc_final: 0.8463 (mmm160) REVERT: F 2163 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7340 (mtp180) REVERT: C 21 MET cc_start: 0.8344 (mmm) cc_final: 0.7863 (mmm) REVERT: C 118 LEU cc_start: 0.9275 (tp) cc_final: 0.9043 (pp) REVERT: C 192 PRO cc_start: 0.9126 (Cg_exo) cc_final: 0.8856 (Cg_endo) REVERT: C 214 LEU cc_start: 0.9352 (mt) cc_final: 0.9078 (mt) REVERT: C 285 MET cc_start: 0.8454 (mmm) cc_final: 0.8196 (mmm) REVERT: C 569 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7054 (mm-30) REVERT: C 626 LYS cc_start: 0.8557 (mmmt) cc_final: 0.7941 (mmmt) REVERT: C 627 LYS cc_start: 0.7511 (tptt) cc_final: 0.7195 (tppt) REVERT: C 715 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8400 (pp) REVERT: G 2015 ASP cc_start: 0.8984 (t70) cc_final: 0.8668 (t0) REVERT: G 2016 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8622 (tptt) REVERT: G 2077 ARG cc_start: 0.8882 (mmt90) cc_final: 0.8500 (mmm160) REVERT: D 21 MET cc_start: 0.8354 (mmm) cc_final: 0.7922 (mmm) REVERT: D 46 LEU cc_start: 0.9032 (mt) cc_final: 0.8805 (pp) REVERT: D 118 LEU cc_start: 0.9245 (tp) cc_final: 0.8901 (pp) REVERT: D 159 PHE cc_start: 0.9046 (t80) cc_final: 0.8728 (t80) REVERT: D 162 LEU cc_start: 0.9378 (mm) cc_final: 0.9017 (pp) REVERT: D 273 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9091 (p) REVERT: D 285 MET cc_start: 0.8469 (mmm) cc_final: 0.8198 (mmm) REVERT: D 303 PHE cc_start: 0.8182 (t80) cc_final: 0.7905 (t80) REVERT: D 386 GLU cc_start: 0.8036 (tp30) cc_final: 0.7801 (tp30) REVERT: D 442 MET cc_start: 0.8691 (tpp) cc_final: 0.8435 (tpp) REVERT: D 626 LYS cc_start: 0.8564 (mmmt) cc_final: 0.7927 (mmmt) REVERT: D 627 LYS cc_start: 0.7697 (tptt) cc_final: 0.7318 (tppt) REVERT: D 691 MET cc_start: 0.8279 (mmt) cc_final: 0.7949 (mmt) REVERT: D 715 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8479 (pp) REVERT: D 878 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 1053 MET cc_start: 0.8578 (mmm) cc_final: 0.8315 (mmm) REVERT: H 2015 ASP cc_start: 0.8926 (t70) cc_final: 0.8602 (t0) REVERT: H 2016 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8462 (tptt) REVERT: H 2077 ARG cc_start: 0.8796 (mmt90) cc_final: 0.8541 (mmm160) outliers start: 79 outliers final: 64 residues processed: 448 average time/residue: 0.4550 time to fit residues: 344.9338 Evaluate side-chains 458 residues out of total 3944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 387 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain E residue 2141 ILE Chi-restraints excluded: chain E residue 2180 THR Chi-restraints excluded: chain E residue 2204 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain F residue 2141 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 617 ASP Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain G residue 2141 ILE Chi-restraints excluded: chain G residue 2180 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain H residue 2180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 7.9990 chunk 371 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 349 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068476 restraints weight = 117408.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070784 restraints weight = 55534.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072308 restraints weight = 35006.962| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37300 Z= 0.145 Angle : 0.551 9.269 50504 Z= 0.267 Chirality : 0.040 0.279 5756 Planarity : 0.003 0.073 6240 Dihedral : 8.526 130.141 5979 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.80 % Allowed : 15.93 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4408 helix: 0.89 (0.12), residues: 1912 sheet: -1.29 (0.20), residues: 640 loop : -0.66 (0.16), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP E2176 HIS 0.006 0.001 HIS B 254 PHE 0.037 0.001 PHE H2023 TYR 0.009 0.001 TYR B 48 ARG 0.004 0.000 ARG D 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7540.87 seconds wall clock time: 137 minutes 42.84 seconds (8262.84 seconds total)