Starting phenix.real_space_refine on Wed Mar 20 11:32:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x59_6704/03_2024/5x59_6704_trim.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17037 2.51 5 N 4401 2.21 5 O 5247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "B" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "C" Number of atoms: 8806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1141, 8800 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 40, 'PCIS': 4, 'PTRANS': 46, 'TRANS': 1050} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8993 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER A 51 " occ=0.54 residue: pdb=" N ASER B 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER B 51 " occ=0.54 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 25.90, per 1000 atoms: 0.97 Number of scatterers: 26838 At special positions: 0 Unit cell: (152.1, 166.4, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5247 8.00 N 4401 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.05 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.01 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.06 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.06 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.05 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.04 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.02 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.01 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " 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 Atom "HETATM26570 O5 NAG B1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26710 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26430 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM26822 O5 NAG C1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26542 O5 NAG A1409 .*. O " rejected from bonding due to valence issues. Atom "HETATM26682 O5 NAG B1409 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 8.8 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6384 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 23.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.676A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.195A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 Processing helix chain 'A' and resid 1018 through 1041 Processing helix chain 'A' and resid 1062 through 1107 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.676A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.613A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.547A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.043A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 824 through 852 removed outlier: 3.638A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.471A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 removed outlier: 3.974A pdb=" N VAL B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 removed outlier: 3.718A pdb=" N SER B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1011 Processing helix chain 'B' and resid 1018 through 1041 Processing helix chain 'B' and resid 1062 through 1107 Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.677A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.196A pdb=" N LEU C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 390' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.612A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.548A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.042A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 824 through 852 removed outlier: 3.639A pdb=" N CYS C 828 " --> pdb=" O TYR C 824 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 940 through 959 removed outlier: 4.472A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 removed outlier: 3.973A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 993 removed outlier: 3.717A pdb=" N SER C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1011 Processing helix chain 'C' and resid 1018 through 1041 Processing helix chain 'C' and resid 1062 through 1107 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP A 34 " --> pdb=" O VAL A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.073A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA A 282 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 618 through 619 Processing sheet with id=AB5, first strand: chain 'A' and resid 779 through 782 removed outlier: 3.562A pdb=" N ILE A 782 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1122 through 1124 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.252A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.072A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.547A pdb=" N ALA B 282 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.160A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.788A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 409 Processing sheet with id=AD1, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AD3, first strand: chain 'B' and resid 779 through 782 removed outlier: 3.561A pdb=" N ILE B 782 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AD5, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.251A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.073A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.548A pdb=" N ALA C 282 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.509A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.858A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.878A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.789A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AE8, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.071A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 619 Processing sheet with id=AF1, first strand: chain 'C' and resid 779 through 782 removed outlier: 3.563A pdb=" N ILE C 782 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 803 through 804 Processing sheet with id=AF3, first strand: chain 'C' and resid 1122 through 1124 840 hydrogen bonds defined for protein. 2241 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: 9.91 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4490 1.32 - 1.45: 7986 1.45 - 1.58: 14761 1.58 - 1.71: 3 1.71 - 1.84: 201 Bond restraints: 27441 Sorted by residual: bond pdb=" N PRO A 59 " pdb=" CD PRO A 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO C 59 " pdb=" CD PRO C 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO B 59 " pdb=" CD PRO B 59 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.69e+01 bond pdb=" CA HIS C 486 " pdb=" C HIS C 486 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.07e+01 bond pdb=" CA HIS B 486 " pdb=" C HIS B 486 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.05e+01 ... (remaining 27436 not shown) Histogram of bond angle deviations from ideal: 97.84 - 106.65: 933 106.65 - 115.46: 16108 115.46 - 124.27: 19493 124.27 - 133.07: 726 133.07 - 141.88: 54 Bond angle restraints: 37314 Sorted by residual: angle pdb=" C SER B1151 " pdb=" N ALA B1152 " pdb=" CA ALA B1152 " ideal model delta sigma weight residual 121.70 140.18 -18.48 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C SER A1151 " pdb=" N ALA A1152 " pdb=" CA ALA A1152 " ideal model delta sigma weight residual 121.70 140.17 -18.47 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C SER C1151 " pdb=" N ALA C1152 " pdb=" CA ALA C1152 " ideal model delta sigma weight residual 121.70 140.15 -18.45 1.80e+00 3.09e-01 1.05e+02 angle pdb=" N SER A 350 " pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 angle pdb=" N SER C 350 " pdb=" CA SER C 350 " pdb=" C SER C 350 " ideal model delta sigma weight residual 110.35 97.96 12.39 1.36e+00 5.41e-01 8.30e+01 ... (remaining 37309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 15944 26.90 - 53.80: 657 53.80 - 80.71: 76 80.71 - 107.61: 9 107.61 - 134.51: 18 Dihedral angle restraints: 16704 sinusoidal: 6714 harmonic: 9990 Sorted by residual: dihedral pdb=" CA SER B 856 " pdb=" C SER B 856 " pdb=" N GLN B 857 " pdb=" CA GLN B 857 " ideal model delta harmonic sigma weight residual -180.00 -45.49 -134.51 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA SER C 856 " pdb=" C SER C 856 " pdb=" N GLN C 857 " pdb=" CA GLN C 857 " ideal model delta harmonic sigma weight residual -180.00 -45.50 -134.50 0 5.00e+00 4.00e-02 7.24e+02 dihedral pdb=" CA SER A 856 " pdb=" C SER A 856 " pdb=" N GLN A 857 " pdb=" CA GLN A 857 " ideal model delta harmonic sigma weight residual -180.00 -45.53 -134.47 0 5.00e+00 4.00e-02 7.23e+02 ... (remaining 16701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3415 0.089 - 0.177: 651 0.177 - 0.266: 140 0.266 - 0.355: 33 0.355 - 0.444: 12 Chirality restraints: 4251 Sorted by residual: chirality pdb=" CA ALA C1018 " pdb=" N ALA C1018 " pdb=" C ALA C1018 " pdb=" CB ALA C1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ALA A1018 " pdb=" N ALA A1018 " pdb=" C ALA A1018 " pdb=" CB ALA A1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA ALA B1018 " pdb=" N ALA B1018 " pdb=" C ALA B1018 " pdb=" CB ALA B1018 " both_signs ideal model delta sigma weight residual False 2.48 2.04 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 4248 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN A 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN A 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN A 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " -0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" CD GLN B 280 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 280 " -0.025 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" CD GLN C 280 " 0.090 2.00e-02 2.50e+03 pdb=" OE1 GLN C 280 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 GLN C 280 " -0.032 2.00e-02 2.50e+03 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 75 2.16 - 2.85: 9668 2.85 - 3.53: 36090 3.53 - 4.22: 66762 4.22 - 4.90: 109335 Nonbonded interactions: 221930 Sorted by model distance: nonbonded pdb=" OE1 GLN B 627 " pdb=" CG2 VAL C 271 " model vdw 1.477 3.460 nonbonded pdb=" OE1 GLN A 627 " pdb=" CG2 VAL B 271 " model vdw 1.498 3.460 nonbonded pdb=" OH TYR B 351 " pdb=" CE1 TYR B 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR A 351 " pdb=" CE1 TYR A 361 " model vdw 1.507 3.340 nonbonded pdb=" OH TYR C 351 " pdb=" CE1 TYR C 361 " model vdw 1.508 3.340 ... (remaining 221925 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 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 1206 or resid 1401 throu \ gh 1410)) } 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=0.46 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: 2.340 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: 0.000 Extract box with map and model: 9.060 Check model and map are aligned: 0.220 Set scattering table: 0.180 Process input model: 85.620 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4126 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 0.141 27441 Z= 0.697 Angle : 1.664 25.582 37314 Z= 0.944 Chirality : 0.080 0.444 4251 Planarity : 0.009 0.114 4779 Dihedral : 15.224 134.510 10212 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 1.33 % Allowed : 13.22 % Favored : 85.45 % Rotamer: Outliers : 4.97 % Allowed : 7.13 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.22 % Twisted Proline : 0.00 % Twisted General : 1.66 % 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: -3.87 (0.12), residues: 3390 helix: -3.00 (0.13), residues: 675 sheet: -1.20 (0.20), residues: 639 loop : -3.02 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP B 960 HIS 0.016 0.004 HIS C1138 PHE 0.038 0.004 PHE C1172 TYR 0.046 0.004 TYR C1171 ARG 0.011 0.001 ARG B 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 619 time to evaluate : 2.816 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7898 (mm) cc_final: 0.7691 (mm) REVERT: A 244 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.5156 (m-40) REVERT: A 614 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7639 (mtp-110) REVERT: A 676 SER cc_start: 0.6027 (m) cc_final: 0.5602 (p) REVERT: A 677 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.5948 (t) REVERT: A 682 ILE cc_start: 0.6125 (pp) cc_final: 0.5754 (tp) REVERT: A 719 ASN cc_start: 0.5494 (m-40) cc_final: 0.5252 (m-40) REVERT: A 726 ASP cc_start: 0.5900 (p0) cc_final: 0.5479 (p0) REVERT: A 827 PHE cc_start: 0.6338 (m-80) cc_final: 0.6085 (m-80) REVERT: A 891 GLU cc_start: 0.7436 (tt0) cc_final: 0.7185 (tt0) REVERT: A 895 PHE cc_start: 0.7791 (m-80) cc_final: 0.7571 (m-80) REVERT: A 900 ILE cc_start: 0.4929 (mp) cc_final: 0.4407 (pt) REVERT: A 907 GLN cc_start: 0.6754 (mt0) cc_final: 0.6551 (pm20) REVERT: A 993 ASN cc_start: 0.8197 (m-40) cc_final: 0.6911 (p0) REVERT: A 1079 ASN cc_start: 0.7890 (t0) cc_final: 0.7604 (m-40) REVERT: B 357 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6423 (mm-30) REVERT: B 473 PHE cc_start: -0.0684 (OUTLIER) cc_final: -0.1183 (t80) REVERT: B 495 LEU cc_start: 0.1133 (OUTLIER) cc_final: 0.0412 (mm) REVERT: B 565 GLU cc_start: 0.3796 (OUTLIER) cc_final: 0.3530 (mt-10) REVERT: B 662 ILE cc_start: 0.4185 (mm) cc_final: 0.3860 (mm) REVERT: B 718 VAL cc_start: 0.6102 (t) cc_final: 0.5860 (t) REVERT: B 725 GLU cc_start: 0.7443 (tp30) cc_final: 0.7162 (tm-30) REVERT: B 807 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6175 (tmtt) REVERT: B 826 GLN cc_start: 0.7221 (mt0) cc_final: 0.7019 (pm20) REVERT: B 848 ASN cc_start: 0.8103 (t160) cc_final: 0.7767 (t0) REVERT: B 1098 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 1203 LYS cc_start: 0.8231 (mttt) cc_final: 0.7896 (tptt) REVERT: C 487 ASN cc_start: 0.3113 (OUTLIER) cc_final: 0.2768 (p0) REVERT: C 489 THR cc_start: 0.3050 (OUTLIER) cc_final: 0.2773 (m) REVERT: C 587 LYS cc_start: 0.4277 (ptmt) cc_final: 0.3771 (tptt) REVERT: C 667 THR cc_start: 0.4942 (p) cc_final: 0.1360 (m) REVERT: C 970 ILE cc_start: 0.5233 (OUTLIER) cc_final: 0.4557 (mt) REVERT: C 990 LEU cc_start: 0.6186 (mt) cc_final: 0.5834 (mp) REVERT: C 992 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6371 (pt0) REVERT: C 1067 ILE cc_start: 0.7840 (mt) cc_final: 0.7410 (mm) REVERT: C 1089 SER cc_start: 0.8468 (t) cc_final: 0.8059 (t) REVERT: C 1098 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.6924 (tp) REVERT: C 1126 PHE cc_start: 0.3930 (m-80) cc_final: 0.3138 (m-10) outliers start: 145 outliers final: 32 residues processed: 746 average time/residue: 0.4030 time to fit residues: 468.2659 Evaluate side-chains 411 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 369 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 1098 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 167 HIS A 298 HIS A 346 GLN A 599 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 792 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A 870 ASN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN A1176 ASN B 236 ASN B 346 GLN B 599 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 792 GLN B 800 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN B 832 ASN B 839 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 ASN B 870 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 ASN B1072 ASN B1104 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 ASN C 199 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 800 GLN C 812 ASN C 832 ASN C 842 GLN C 870 ASN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1028 ASN C1104 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4531 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27441 Z= 0.279 Angle : 1.031 16.247 37314 Z= 0.528 Chirality : 0.057 0.452 4251 Planarity : 0.007 0.113 4779 Dihedral : 10.795 100.005 4423 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.00 % Favored : 88.70 % Rotamer: Outliers : 3.70 % Allowed : 13.77 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.89 % 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: -3.06 (0.13), residues: 3390 helix: -1.38 (0.17), residues: 684 sheet: -0.66 (0.22), residues: 597 loop : -2.85 (0.12), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 310 HIS 0.019 0.002 HIS C 670 PHE 0.035 0.002 PHE C 327 TYR 0.034 0.003 TYR B1153 ARG 0.015 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 437 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7510 (tp30) REVERT: A 587 LYS cc_start: 0.6370 (ptmt) cc_final: 0.5301 (tppt) REVERT: A 631 VAL cc_start: 0.6603 (OUTLIER) cc_final: 0.6356 (m) REVERT: A 633 ASP cc_start: 0.7964 (t0) cc_final: 0.6189 (p0) REVERT: A 682 ILE cc_start: 0.6399 (pp) cc_final: 0.6039 (tp) REVERT: A 726 ASP cc_start: 0.5735 (p0) cc_final: 0.5384 (p0) REVERT: A 841 ARG cc_start: 0.6628 (mtp-110) cc_final: 0.6194 (ptm-80) REVERT: A 891 GLU cc_start: 0.7647 (tt0) cc_final: 0.7228 (tt0) REVERT: A 895 PHE cc_start: 0.8074 (m-80) cc_final: 0.7516 (m-80) REVERT: A 993 ASN cc_start: 0.8229 (m-40) cc_final: 0.7158 (p0) REVERT: A 1079 ASN cc_start: 0.8018 (t0) cc_final: 0.7776 (m-40) REVERT: B 85 TYR cc_start: 0.8061 (m-80) cc_final: 0.7784 (m-80) REVERT: B 252 GLU cc_start: 0.6987 (pt0) cc_final: 0.6594 (pt0) REVERT: B 310 TRP cc_start: 0.5598 (m-90) cc_final: 0.5360 (m-90) REVERT: B 323 PHE cc_start: 0.7344 (m-10) cc_final: 0.7103 (m-10) REVERT: B 343 ASP cc_start: 0.7513 (m-30) cc_final: 0.7277 (p0) REVERT: B 345 SER cc_start: 0.7501 (p) cc_final: 0.7262 (m) REVERT: B 473 PHE cc_start: -0.0555 (OUTLIER) cc_final: -0.1120 (t80) REVERT: B 487 ASN cc_start: 0.0104 (OUTLIER) cc_final: -0.1966 (t0) REVERT: B 565 GLU cc_start: 0.3560 (OUTLIER) cc_final: 0.3224 (mt-10) REVERT: B 807 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6747 (tmtt) REVERT: B 820 LEU cc_start: 0.7751 (mt) cc_final: 0.7541 (mm) REVERT: B 887 ARG cc_start: 0.6539 (tpp80) cc_final: 0.6296 (mmm-85) REVERT: B 906 MET cc_start: 0.4240 (tpt) cc_final: 0.3908 (tpt) REVERT: B 913 MET cc_start: 0.7059 (tpt) cc_final: 0.6428 (ttt) REVERT: B 938 LEU cc_start: 0.8097 (tt) cc_final: 0.7873 (tp) REVERT: B 1009 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 1119 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7266 (mt0) REVERT: C 58 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4853 (t80) REVERT: C 161 MET cc_start: -0.0916 (mmt) cc_final: -0.2016 (ptm) REVERT: C 587 LYS cc_start: 0.4141 (ptmt) cc_final: 0.3565 (tptt) REVERT: C 667 THR cc_start: 0.5222 (p) cc_final: 0.3563 (m) REVERT: C 719 ASN cc_start: 0.3655 (m-40) cc_final: 0.3289 (t0) REVERT: C 819 GLN cc_start: 0.7405 (mt0) cc_final: 0.6675 (tp-100) REVERT: C 910 ASP cc_start: 0.5979 (m-30) cc_final: 0.5691 (p0) REVERT: C 992 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5920 (mt-10) REVERT: C 1098 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 1105 GLU cc_start: 0.7271 (tp30) cc_final: 0.6889 (pt0) REVERT: C 1200 LEU cc_start: 0.8315 (tp) cc_final: 0.8010 (tt) outliers start: 108 outliers final: 56 residues processed: 519 average time/residue: 0.3638 time to fit residues: 303.1481 Evaluate side-chains 389 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 326 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 311 optimal weight: 0.7980 chunk 336 optimal weight: 4.9990 chunk 277 optimal weight: 30.0000 chunk 308 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 602 ASN A 619 ASN A 733 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN A1129 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 36 GLN B 91 HIS B 346 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 733 GLN C 769 GLN C 832 ASN C1009 GLN C1023 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 27441 Z= 0.282 Angle : 0.998 19.677 37314 Z= 0.505 Chirality : 0.055 0.328 4251 Planarity : 0.006 0.107 4779 Dihedral : 8.122 76.750 4376 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.07 % Favored : 86.63 % Rotamer: Outliers : 3.70 % Allowed : 15.79 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.68 % Twisted General : 0.64 % 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: -2.64 (0.13), residues: 3390 helix: -0.52 (0.18), residues: 684 sheet: -0.82 (0.20), residues: 678 loop : -2.67 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 310 HIS 0.010 0.002 HIS C 348 PHE 0.034 0.002 PHE A 323 TYR 0.028 0.002 TYR A 641 ARG 0.008 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 371 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.4279 (tpt) cc_final: 0.3879 (tpt) REVERT: A 587 LYS cc_start: 0.6431 (ptmt) cc_final: 0.5396 (tppt) REVERT: A 633 ASP cc_start: 0.7865 (t0) cc_final: 0.6144 (p0) REVERT: A 682 ILE cc_start: 0.6435 (pp) cc_final: 0.5912 (tp) REVERT: A 726 ASP cc_start: 0.6407 (p0) cc_final: 0.5963 (p0) REVERT: A 799 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7223 (pt) REVERT: A 895 PHE cc_start: 0.8124 (m-80) cc_final: 0.7518 (m-80) REVERT: A 902 ASP cc_start: 0.6030 (m-30) cc_final: 0.5829 (t70) REVERT: A 993 ASN cc_start: 0.8265 (m-40) cc_final: 0.7300 (p0) REVERT: A 1079 ASN cc_start: 0.8250 (t0) cc_final: 0.7957 (m-40) REVERT: A 1100 LYS cc_start: 0.7498 (tttt) cc_final: 0.7225 (tttp) REVERT: A 1129 ASN cc_start: 0.8074 (t0) cc_final: 0.7867 (t0) REVERT: B 310 TRP cc_start: 0.5711 (m-90) cc_final: 0.5403 (m-90) REVERT: B 473 PHE cc_start: -0.0469 (OUTLIER) cc_final: -0.1139 (t80) REVERT: B 633 ASP cc_start: 0.5815 (m-30) cc_final: 0.5202 (p0) REVERT: B 719 ASN cc_start: 0.6931 (m-40) cc_final: 0.6129 (p0) REVERT: B 807 LYS cc_start: 0.7172 (mtmt) cc_final: 0.6777 (tmtt) REVERT: B 938 LEU cc_start: 0.8645 (tt) cc_final: 0.8393 (tp) REVERT: B 1068 ASP cc_start: 0.8336 (m-30) cc_final: 0.7916 (t0) REVERT: B 1119 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7812 (mt0) REVERT: B 1169 ASN cc_start: 0.7455 (p0) cc_final: 0.6996 (p0) REVERT: B 1204 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: C 58 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.5438 (t80) REVERT: C 161 MET cc_start: -0.0575 (mmt) cc_final: -0.2055 (ptm) REVERT: C 290 ILE cc_start: 0.5219 (mm) cc_final: 0.4849 (mt) REVERT: C 563 MET cc_start: 0.1326 (mmm) cc_final: 0.0044 (tpt) REVERT: C 587 LYS cc_start: 0.4624 (ptmt) cc_final: 0.3737 (tptt) REVERT: C 733 GLN cc_start: 0.3858 (OUTLIER) cc_final: 0.3320 (pm20) REVERT: C 848 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7404 (p0) REVERT: C 943 MET cc_start: 0.7225 (ptm) cc_final: 0.6809 (ptm) REVERT: C 970 ILE cc_start: 0.5037 (OUTLIER) cc_final: 0.4722 (mm) REVERT: C 1035 LYS cc_start: 0.7231 (tmtt) cc_final: 0.6819 (mmtt) REVERT: C 1098 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8123 (tp) outliers start: 108 outliers final: 59 residues processed: 452 average time/residue: 0.3487 time to fit residues: 255.1925 Evaluate side-chains 366 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 299 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 733 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 312 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 163 optimal weight: 0.0670 chunk 295 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 988 GLN A1028 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 125 ASN B 167 HIS ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN C 319 GLN C 501 ASN ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27441 Z= 0.217 Angle : 0.908 17.677 37314 Z= 0.457 Chirality : 0.051 0.281 4251 Planarity : 0.006 0.100 4779 Dihedral : 7.269 56.195 4367 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.77 % Favored : 87.96 % Rotamer: Outliers : 3.22 % Allowed : 17.47 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.49 % 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: -2.36 (0.14), residues: 3390 helix: -0.01 (0.19), residues: 684 sheet: -0.54 (0.21), residues: 660 loop : -2.63 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1184 HIS 0.006 0.001 HIS C 836 PHE 0.041 0.002 PHE A 778 TYR 0.030 0.002 TYR A 641 ARG 0.005 0.001 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 342 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.4311 (tpp) cc_final: 0.3987 (tpp) REVERT: A 587 LYS cc_start: 0.6549 (ptmt) cc_final: 0.5404 (tppt) REVERT: A 633 ASP cc_start: 0.7933 (t0) cc_final: 0.6266 (p0) REVERT: A 682 ILE cc_start: 0.6529 (pp) cc_final: 0.5969 (tp) REVERT: A 726 ASP cc_start: 0.6555 (p0) cc_final: 0.6262 (p0) REVERT: A 799 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7321 (pt) REVERT: A 841 ARG cc_start: 0.7168 (mtp-110) cc_final: 0.6961 (ptm-80) REVERT: A 849 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7299 (tp) REVERT: A 895 PHE cc_start: 0.8068 (m-80) cc_final: 0.7320 (m-80) REVERT: A 902 ASP cc_start: 0.5672 (m-30) cc_final: 0.5403 (t70) REVERT: A 960 TRP cc_start: 0.1258 (t60) cc_final: 0.0694 (t60) REVERT: A 988 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7166 (pt0) REVERT: A 993 ASN cc_start: 0.8300 (m-40) cc_final: 0.7470 (p0) REVERT: A 1100 LYS cc_start: 0.8304 (tttt) cc_final: 0.8041 (tttm) REVERT: A 1129 ASN cc_start: 0.7905 (t0) cc_final: 0.7568 (t0) REVERT: B 310 TRP cc_start: 0.5621 (m-90) cc_final: 0.5389 (m-90) REVERT: B 473 PHE cc_start: -0.0552 (OUTLIER) cc_final: -0.1181 (t80) REVERT: B 633 ASP cc_start: 0.6544 (m-30) cc_final: 0.5822 (p0) REVERT: B 694 ARG cc_start: 0.7534 (mtt180) cc_final: 0.6852 (mtm110) REVERT: B 715 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5612 (tp) REVERT: B 719 ASN cc_start: 0.6743 (m-40) cc_final: 0.5952 (p0) REVERT: B 807 LYS cc_start: 0.7325 (mtmt) cc_final: 0.6923 (tmtt) REVERT: B 938 LEU cc_start: 0.8451 (tt) cc_final: 0.8185 (tp) REVERT: B 1119 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7985 (mt0) REVERT: C 58 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.5903 (t80) REVERT: C 161 MET cc_start: -0.0671 (mmt) cc_final: -0.2071 (ptm) REVERT: C 563 MET cc_start: 0.1701 (mmm) cc_final: 0.1125 (mtm) REVERT: C 587 LYS cc_start: 0.4512 (ptmt) cc_final: 0.3639 (tptt) REVERT: C 733 GLN cc_start: 0.3204 (OUTLIER) cc_final: 0.1426 (pm20) REVERT: C 848 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7901 (t0) REVERT: C 849 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7595 (tp) REVERT: C 943 MET cc_start: 0.7854 (ptm) cc_final: 0.7342 (ttp) REVERT: C 1008 MET cc_start: 0.6170 (ttp) cc_final: 0.4148 (tmm) REVERT: C 1035 LYS cc_start: 0.7074 (tmtt) cc_final: 0.6723 (mmmt) REVERT: C 1098 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (tt) REVERT: C 1105 GLU cc_start: 0.7943 (tp30) cc_final: 0.7265 (pt0) REVERT: C 1192 TYR cc_start: 0.5306 (t80) cc_final: 0.5106 (t80) outliers start: 94 outliers final: 54 residues processed: 412 average time/residue: 0.3475 time to fit residues: 233.7261 Evaluate side-chains 372 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 308 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1147 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 733 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1173 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 50.0000 chunk 187 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 785 ASN ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 819 GLN B 839 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 91 HIS C 236 ASN C 670 HIS C 836 HIS ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1027 ASN C1132 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 27441 Z= 0.444 Angle : 1.109 21.018 37314 Z= 0.569 Chirality : 0.059 0.454 4251 Planarity : 0.007 0.104 4779 Dihedral : 8.265 56.089 4364 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.29 % Favored : 85.36 % Rotamer: Outliers : 3.94 % Allowed : 17.61 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -2.92 (0.13), residues: 3390 helix: -0.56 (0.18), residues: 663 sheet: -1.18 (0.21), residues: 666 loop : -2.83 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 310 HIS 0.021 0.002 HIS C1138 PHE 0.045 0.003 PHE A 323 TYR 0.037 0.003 TYR A 641 ARG 0.007 0.001 ARG C 979 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 388 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9179 (mm) cc_final: 0.8891 (mm) REVERT: A 58 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: A 240 MET cc_start: 0.5769 (tpt) cc_final: 0.5397 (tpt) REVERT: A 267 SER cc_start: 0.8337 (t) cc_final: 0.8103 (p) REVERT: A 563 MET cc_start: 0.2626 (ttt) cc_final: 0.2283 (ttp) REVERT: A 587 LYS cc_start: 0.6619 (ptmt) cc_final: 0.5284 (tppt) REVERT: A 633 ASP cc_start: 0.8186 (t0) cc_final: 0.6508 (p0) REVERT: A 726 ASP cc_start: 0.7835 (p0) cc_final: 0.7234 (p0) REVERT: A 819 GLN cc_start: 0.6891 (mt0) cc_final: 0.5925 (mm-40) REVERT: A 831 ILE cc_start: 0.8083 (mm) cc_final: 0.7464 (mm) REVERT: A 844 ASP cc_start: 0.8688 (t70) cc_final: 0.8300 (t70) REVERT: A 848 ASN cc_start: 0.8520 (t0) cc_final: 0.8252 (p0) REVERT: A 924 ILE cc_start: 0.5960 (mt) cc_final: 0.5654 (mp) REVERT: A 938 LEU cc_start: 0.9378 (tt) cc_final: 0.9083 (tt) REVERT: A 993 ASN cc_start: 0.8129 (m-40) cc_final: 0.7311 (p0) REVERT: A 1056 GLN cc_start: 0.4790 (mt0) cc_final: 0.4155 (mp10) REVERT: A 1067 ILE cc_start: 0.6932 (mm) cc_final: 0.6396 (mt) REVERT: A 1079 ASN cc_start: 0.8797 (t0) cc_final: 0.8482 (m-40) REVERT: B 253 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.7118 (m-10) REVERT: B 473 PHE cc_start: -0.0059 (OUTLIER) cc_final: -0.0693 (m-80) REVERT: B 633 ASP cc_start: 0.7655 (m-30) cc_final: 0.7042 (p0) REVERT: B 665 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7440 (pttm) REVERT: B 694 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6936 (mtm110) REVERT: B 696 MET cc_start: 0.6492 (mmt) cc_final: 0.5809 (mtm) REVERT: B 793 GLU cc_start: 0.8910 (pt0) cc_final: 0.8681 (pm20) REVERT: B 807 LYS cc_start: 0.7400 (mtmt) cc_final: 0.7169 (tmtt) REVERT: B 978 TYR cc_start: 0.8079 (m-80) cc_final: 0.7843 (m-80) REVERT: B 1068 ASP cc_start: 0.8560 (m-30) cc_final: 0.8198 (t0) REVERT: B 1119 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8512 (mt0) REVERT: C 56 ILE cc_start: 0.8786 (mm) cc_final: 0.8500 (mm) REVERT: C 58 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7665 (t80) REVERT: C 161 MET cc_start: -0.0412 (mmt) cc_final: -0.1729 (ptm) REVERT: C 341 PHE cc_start: 0.7546 (t80) cc_final: 0.6957 (t80) REVERT: C 599 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5479 (mt0) REVERT: C 633 ASP cc_start: 0.7580 (m-30) cc_final: 0.5897 (p0) REVERT: C 848 ASN cc_start: 0.8688 (t0) cc_final: 0.8207 (p0) REVERT: C 924 ILE cc_start: 0.5361 (pt) cc_final: 0.4925 (pt) REVERT: C 978 TYR cc_start: 0.8215 (m-10) cc_final: 0.7995 (m-10) REVERT: C 1035 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7239 (mmmt) REVERT: C 1184 TRP cc_start: 0.7780 (p-90) cc_final: 0.7539 (p-90) REVERT: C 1192 TYR cc_start: 0.7091 (t80) cc_final: 0.6779 (t80) outliers start: 115 outliers final: 67 residues processed: 472 average time/residue: 0.3653 time to fit residues: 281.4449 Evaluate side-chains 384 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 311 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1041 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 253 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1153 TYR Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 670 HIS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1027 ASN Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 0.0970 chunk 297 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 274 optimal weight: 0.3980 chunk 153 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 173 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 681 HIS A 785 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN B 36 GLN B 319 GLN B 501 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN B 839 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 GLN C1027 ASN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5489 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27441 Z= 0.225 Angle : 0.929 17.071 37314 Z= 0.468 Chirality : 0.052 0.284 4251 Planarity : 0.006 0.109 4779 Dihedral : 7.194 59.082 4356 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.71 % Favored : 87.96 % Rotamer: Outliers : 2.77 % Allowed : 20.35 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.52 % 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: -2.40 (0.14), residues: 3390 helix: 0.28 (0.20), residues: 663 sheet: -0.70 (0.21), residues: 633 loop : -2.69 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 310 HIS 0.025 0.002 HIS C 670 PHE 0.050 0.002 PHE C1172 TYR 0.032 0.002 TYR A 606 ARG 0.006 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 355 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TYR cc_start: 0.4711 (m-10) cc_final: 0.4480 (m-10) REVERT: A 563 MET cc_start: 0.2342 (ttt) cc_final: 0.1957 (ttp) REVERT: A 587 LYS cc_start: 0.6807 (ptmt) cc_final: 0.5473 (tppt) REVERT: A 633 ASP cc_start: 0.8186 (t0) cc_final: 0.6764 (p0) REVERT: A 725 GLU cc_start: 0.6146 (tp30) cc_final: 0.5731 (tp30) REVERT: A 726 ASP cc_start: 0.7710 (p0) cc_final: 0.7121 (p0) REVERT: A 773 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 819 GLN cc_start: 0.6903 (mt0) cc_final: 0.6011 (mm-40) REVERT: A 940 ASP cc_start: 0.6297 (m-30) cc_final: 0.5830 (m-30) REVERT: A 993 ASN cc_start: 0.8282 (m-40) cc_final: 0.7607 (p0) REVERT: A 1084 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 1174 LYS cc_start: 0.4780 (mttt) cc_final: 0.3763 (tptp) REVERT: B 330 ASP cc_start: 0.7295 (p0) cc_final: 0.7042 (t70) REVERT: B 473 PHE cc_start: -0.0099 (OUTLIER) cc_final: -0.0696 (m-80) REVERT: B 633 ASP cc_start: 0.8130 (m-30) cc_final: 0.7344 (p0) REVERT: B 696 MET cc_start: 0.6223 (mmt) cc_final: 0.5522 (mtm) REVERT: B 807 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7052 (tmtt) REVERT: B 978 TYR cc_start: 0.8174 (m-80) cc_final: 0.7919 (m-80) REVERT: B 1068 ASP cc_start: 0.8496 (m-30) cc_final: 0.8192 (t0) REVERT: B 1150 VAL cc_start: 0.7391 (t) cc_final: 0.7157 (p) REVERT: C 56 ILE cc_start: 0.8537 (mm) cc_final: 0.8290 (mm) REVERT: C 58 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7387 (t80) REVERT: C 161 MET cc_start: -0.0637 (mmt) cc_final: -0.1838 (ptm) REVERT: C 563 MET cc_start: 0.2119 (mmm) cc_final: 0.0932 (mtp) REVERT: C 633 ASP cc_start: 0.7927 (m-30) cc_final: 0.6322 (p0) REVERT: C 673 LEU cc_start: 0.7494 (tt) cc_final: 0.7046 (tp) REVERT: C 978 TYR cc_start: 0.8248 (m-10) cc_final: 0.7983 (m-10) REVERT: C 1035 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7123 (mmmt) REVERT: C 1084 GLN cc_start: 0.8250 (tp40) cc_final: 0.7915 (tt0) REVERT: C 1174 LYS cc_start: 0.5261 (mttt) cc_final: 0.4212 (tptm) outliers start: 81 outliers final: 48 residues processed: 414 average time/residue: 0.3543 time to fit residues: 237.8128 Evaluate side-chains 348 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1114 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 3.9990 chunk 37 optimal weight: 0.0030 chunk 188 optimal weight: 0.6980 chunk 241 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 278 optimal weight: 30.0000 chunk 184 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN A 988 GLN A1176 ASN B 280 GLN B 319 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN C1023 GLN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.8567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27441 Z= 0.231 Angle : 0.907 16.452 37314 Z= 0.456 Chirality : 0.051 0.277 4251 Planarity : 0.006 0.104 4779 Dihedral : 6.903 59.524 4356 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.45 % Favored : 87.31 % Rotamer: Outliers : 2.77 % Allowed : 20.97 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.68 % Twisted Proline : 0.68 % Twisted General : 0.46 % 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: -2.34 (0.14), residues: 3390 helix: 0.35 (0.20), residues: 663 sheet: -0.67 (0.22), residues: 615 loop : -2.63 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 310 HIS 0.016 0.001 HIS A 681 PHE 0.032 0.002 PHE A 778 TYR 0.032 0.002 TYR A 641 ARG 0.012 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 314 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9038 (mm) cc_final: 0.8747 (mm) REVERT: A 58 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: A 87 TYR cc_start: 0.4888 (m-10) cc_final: 0.4659 (m-10) REVERT: A 563 MET cc_start: 0.2327 (ttt) cc_final: 0.2019 (ttp) REVERT: A 587 LYS cc_start: 0.6758 (ptmt) cc_final: 0.5414 (tppt) REVERT: A 633 ASP cc_start: 0.8154 (t0) cc_final: 0.6651 (p0) REVERT: A 674 PHE cc_start: 0.8353 (m-80) cc_final: 0.8079 (m-10) REVERT: A 725 GLU cc_start: 0.6168 (tp30) cc_final: 0.5786 (tp30) REVERT: A 726 ASP cc_start: 0.8328 (p0) cc_final: 0.7715 (p0) REVERT: A 729 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4948 (mp) REVERT: A 773 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 819 GLN cc_start: 0.6849 (mt0) cc_final: 0.5825 (mm-40) REVERT: A 927 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: A 940 ASP cc_start: 0.6135 (m-30) cc_final: 0.5743 (m-30) REVERT: A 970 ILE cc_start: 0.5466 (mm) cc_final: 0.4859 (mm) REVERT: A 993 ASN cc_start: 0.8266 (m-40) cc_final: 0.7559 (p0) REVERT: A 994 GLN cc_start: 0.7554 (mt0) cc_final: 0.7166 (pm20) REVERT: A 1008 MET cc_start: 0.5370 (mmt) cc_final: 0.5160 (mmt) REVERT: A 1084 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8208 (tt0) REVERT: A 1174 LYS cc_start: 0.4589 (mttt) cc_final: 0.3527 (tptp) REVERT: A 1196 PRO cc_start: 0.7321 (Cg_exo) cc_final: 0.7094 (Cg_endo) REVERT: B 330 ASP cc_start: 0.7263 (p0) cc_final: 0.6986 (t70) REVERT: B 473 PHE cc_start: 0.0038 (OUTLIER) cc_final: -0.0608 (m-80) REVERT: B 633 ASP cc_start: 0.8188 (m-30) cc_final: 0.7547 (p0) REVERT: B 665 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7625 (pttp) REVERT: B 696 MET cc_start: 0.6349 (mmt) cc_final: 0.5646 (mtm) REVERT: B 733 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.6847 (pp30) REVERT: B 807 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7015 (tmtt) REVERT: B 843 ASP cc_start: 0.8298 (m-30) cc_final: 0.8026 (t0) REVERT: B 941 VAL cc_start: 0.8873 (m) cc_final: 0.8590 (p) REVERT: B 1068 ASP cc_start: 0.8627 (m-30) cc_final: 0.8248 (t0) REVERT: B 1150 VAL cc_start: 0.7513 (t) cc_final: 0.7263 (p) REVERT: C 58 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7520 (t80) REVERT: C 110 LYS cc_start: 0.3810 (ttmt) cc_final: 0.3519 (ttmt) REVERT: C 161 MET cc_start: -0.0430 (mmt) cc_final: -0.1989 (ptm) REVERT: C 240 MET cc_start: 0.2770 (mtt) cc_final: 0.1336 (mmp) REVERT: C 563 MET cc_start: 0.1796 (mmm) cc_final: 0.0729 (mtp) REVERT: C 633 ASP cc_start: 0.8133 (m-30) cc_final: 0.6576 (p0) REVERT: C 696 MET cc_start: 0.4570 (mmm) cc_final: 0.4359 (mtm) REVERT: C 757 MET cc_start: 0.6855 (tpt) cc_final: 0.6521 (tpt) REVERT: C 978 TYR cc_start: 0.8280 (m-10) cc_final: 0.7981 (m-10) REVERT: C 1084 GLN cc_start: 0.8444 (tp40) cc_final: 0.8121 (tt0) REVERT: C 1098 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8630 (tp) REVERT: C 1174 LYS cc_start: 0.5109 (mttt) cc_final: 0.4158 (tptm) outliers start: 81 outliers final: 49 residues processed: 380 average time/residue: 0.3381 time to fit residues: 212.7247 Evaluate side-chains 350 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 292 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 870 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1181 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN A 927 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1176 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.8818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27441 Z= 0.221 Angle : 0.898 15.923 37314 Z= 0.451 Chirality : 0.051 0.284 4251 Planarity : 0.006 0.111 4779 Dihedral : 6.805 58.317 4355 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.22 % Favored : 87.52 % Rotamer: Outliers : 2.74 % Allowed : 21.03 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.62 % Twisted Proline : 1.36 % Twisted General : 0.46 % 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: -2.30 (0.14), residues: 3390 helix: 0.38 (0.20), residues: 669 sheet: -0.69 (0.21), residues: 627 loop : -2.61 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 310 HIS 0.012 0.001 HIS A 681 PHE 0.034 0.002 PHE A 254 TYR 0.043 0.002 TYR B 642 ARG 0.008 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 309 time to evaluate : 2.783 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9003 (mm) cc_final: 0.8725 (mm) REVERT: A 58 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: A 563 MET cc_start: 0.2484 (ttt) cc_final: 0.2201 (ttp) REVERT: A 587 LYS cc_start: 0.6828 (ptmt) cc_final: 0.5520 (tppt) REVERT: A 633 ASP cc_start: 0.8153 (t0) cc_final: 0.6529 (p0) REVERT: A 674 PHE cc_start: 0.8347 (m-80) cc_final: 0.7938 (m-10) REVERT: A 725 GLU cc_start: 0.6339 (tp30) cc_final: 0.6027 (tp30) REVERT: A 726 ASP cc_start: 0.8283 (p0) cc_final: 0.7707 (p0) REVERT: A 729 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.5008 (mp) REVERT: A 773 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 843 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 927 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: A 940 ASP cc_start: 0.6112 (m-30) cc_final: 0.5700 (m-30) REVERT: A 970 ILE cc_start: 0.5502 (mm) cc_final: 0.5209 (mm) REVERT: A 993 ASN cc_start: 0.8237 (m-40) cc_final: 0.7692 (p0) REVERT: A 994 GLN cc_start: 0.7449 (mt0) cc_final: 0.7133 (pm20) REVERT: A 1084 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 1090 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7601 (tm-30) REVERT: A 1116 PHE cc_start: 0.5720 (m-80) cc_final: 0.5477 (m-80) REVERT: A 1174 LYS cc_start: 0.4517 (mttt) cc_final: 0.3460 (tptp) REVERT: B 252 GLU cc_start: 0.7472 (tt0) cc_final: 0.7057 (tt0) REVERT: B 310 TRP cc_start: 0.6082 (m-90) cc_final: 0.5839 (m-90) REVERT: B 330 ASP cc_start: 0.7227 (p0) cc_final: 0.7023 (t70) REVERT: B 473 PHE cc_start: -0.0064 (OUTLIER) cc_final: -0.0699 (m-80) REVERT: B 633 ASP cc_start: 0.8273 (m-30) cc_final: 0.7498 (p0) REVERT: B 696 MET cc_start: 0.6440 (mmt) cc_final: 0.6143 (mmm) REVERT: B 733 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.6657 (pp30) REVERT: B 807 LYS cc_start: 0.7491 (mtmt) cc_final: 0.7133 (tmtt) REVERT: B 821 LEU cc_start: 0.7494 (pp) cc_final: 0.6804 (tp) REVERT: B 843 ASP cc_start: 0.8257 (m-30) cc_final: 0.8048 (t0) REVERT: B 1068 ASP cc_start: 0.8586 (m-30) cc_final: 0.8228 (t0) REVERT: C 58 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7348 (t80) REVERT: C 110 LYS cc_start: 0.4284 (ttmt) cc_final: 0.4050 (ttmt) REVERT: C 161 MET cc_start: -0.0757 (mmt) cc_final: -0.1630 (mmm) REVERT: C 240 MET cc_start: 0.2715 (mtt) cc_final: 0.1383 (mmp) REVERT: C 563 MET cc_start: 0.1664 (mmm) cc_final: 0.0642 (mtp) REVERT: C 633 ASP cc_start: 0.8081 (m-30) cc_final: 0.6678 (p0) REVERT: C 673 LEU cc_start: 0.7231 (tt) cc_final: 0.6863 (tp) REVERT: C 978 TYR cc_start: 0.8213 (m-10) cc_final: 0.7916 (m-10) REVERT: C 1098 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8622 (tp) REVERT: C 1174 LYS cc_start: 0.5024 (mttt) cc_final: 0.4095 (tptm) outliers start: 80 outliers final: 56 residues processed: 369 average time/residue: 0.3497 time to fit residues: 213.2398 Evaluate side-chains 345 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 870 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1181 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.0770 chunk 315 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 277 optimal weight: 0.0470 chunk 290 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 842 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 ASN B 733 GLN B 800 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 769 GLN C 842 GLN C1023 GLN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.8985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27441 Z= 0.213 Angle : 0.890 15.768 37314 Z= 0.447 Chirality : 0.050 0.277 4251 Planarity : 0.006 0.110 4779 Dihedral : 6.626 57.799 4355 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.36 % Favored : 87.40 % Rotamer: Outliers : 2.19 % Allowed : 21.96 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 0.68 % Twisted General : 0.40 % 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: -2.27 (0.14), residues: 3390 helix: 0.51 (0.20), residues: 666 sheet: -0.83 (0.20), residues: 690 loop : -2.61 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 310 HIS 0.011 0.001 HIS A 681 PHE 0.029 0.002 PHE A 674 TYR 0.048 0.002 TYR B 642 ARG 0.015 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9014 (mm) cc_final: 0.8748 (mm) REVERT: A 58 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: A 87 TYR cc_start: 0.5118 (m-10) cc_final: 0.4901 (m-10) REVERT: A 452 MET cc_start: 0.0781 (mtm) cc_final: 0.0167 (mmt) REVERT: A 563 MET cc_start: 0.2486 (ttt) cc_final: 0.2174 (ttp) REVERT: A 587 LYS cc_start: 0.6838 (ptmt) cc_final: 0.5538 (tppt) REVERT: A 633 ASP cc_start: 0.8186 (t0) cc_final: 0.6576 (p0) REVERT: A 650 CYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6577 (t) REVERT: A 729 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4664 (mp) REVERT: A 773 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7784 (tt) REVERT: A 843 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7868 (t0) REVERT: A 913 MET cc_start: 0.7552 (tpt) cc_final: 0.6792 (ptt) REVERT: A 932 TYR cc_start: 0.7940 (p90) cc_final: 0.7518 (p90) REVERT: A 940 ASP cc_start: 0.6053 (m-30) cc_final: 0.5635 (m-30) REVERT: A 970 ILE cc_start: 0.5352 (mm) cc_final: 0.4975 (mm) REVERT: A 993 ASN cc_start: 0.8250 (m-40) cc_final: 0.7740 (p0) REVERT: A 994 GLN cc_start: 0.7455 (mt0) cc_final: 0.7194 (pm20) REVERT: A 1084 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8063 (tt0) REVERT: A 1116 PHE cc_start: 0.5809 (m-80) cc_final: 0.5591 (m-80) REVERT: A 1174 LYS cc_start: 0.4375 (mttt) cc_final: 0.3437 (tptp) REVERT: B 310 TRP cc_start: 0.6000 (m-90) cc_final: 0.5782 (m-90) REVERT: B 473 PHE cc_start: -0.0064 (OUTLIER) cc_final: -0.0749 (t80) REVERT: B 633 ASP cc_start: 0.8085 (m-30) cc_final: 0.7494 (p0) REVERT: B 696 MET cc_start: 0.6250 (mmt) cc_final: 0.5915 (mmm) REVERT: B 821 LEU cc_start: 0.7527 (pp) cc_final: 0.6869 (tp) REVERT: B 843 ASP cc_start: 0.8331 (m-30) cc_final: 0.7987 (t0) REVERT: B 1068 ASP cc_start: 0.8567 (m-30) cc_final: 0.8264 (t0) REVERT: B 1112 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7943 (mppt) REVERT: C 58 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7506 (t80) REVERT: C 161 MET cc_start: -0.1095 (mmt) cc_final: -0.1901 (mmm) REVERT: C 240 MET cc_start: 0.2667 (mtt) cc_final: 0.1085 (mmp) REVERT: C 361 TYR cc_start: 0.7931 (m-80) cc_final: 0.7646 (m-80) REVERT: C 510 ASP cc_start: 0.2175 (OUTLIER) cc_final: 0.1792 (m-30) REVERT: C 563 MET cc_start: 0.1668 (mmm) cc_final: 0.0797 (mtp) REVERT: C 633 ASP cc_start: 0.8093 (m-30) cc_final: 0.6684 (p0) REVERT: C 673 LEU cc_start: 0.7209 (tt) cc_final: 0.6884 (tp) REVERT: C 696 MET cc_start: 0.4659 (mtm) cc_final: 0.4279 (mmm) REVERT: C 717 LEU cc_start: 0.5994 (tm) cc_final: 0.5791 (tm) REVERT: C 978 TYR cc_start: 0.8197 (m-10) cc_final: 0.7911 (m-10) REVERT: C 1098 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8598 (tp) REVERT: C 1174 LYS cc_start: 0.5393 (mttt) cc_final: 0.4498 (tptm) outliers start: 64 outliers final: 48 residues processed: 354 average time/residue: 0.3550 time to fit residues: 206.9787 Evaluate side-chains 335 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 278 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 842 GLN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1023 GLN Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 225 optimal weight: 0.8980 chunk 340 optimal weight: 0.7980 chunk 313 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 209 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 833 GLN A 842 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.9000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 27441 Z= 0.322 Angle : 1.105 59.197 37314 Z= 0.607 Chirality : 0.054 1.168 4251 Planarity : 0.006 0.111 4779 Dihedral : 6.638 57.733 4355 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.39 % Favored : 87.40 % Rotamer: Outliers : 2.12 % Allowed : 22.37 % Favored : 75.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.40 % 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: -2.29 (0.14), residues: 3390 helix: 0.42 (0.20), residues: 669 sheet: -0.82 (0.20), residues: 690 loop : -2.60 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 310 HIS 0.007 0.001 HIS A 681 PHE 0.029 0.002 PHE A 116 TYR 0.053 0.002 TYR C 642 ARG 0.007 0.001 ARG A 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 276 time to evaluate : 3.293 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.9009 (mm) cc_final: 0.8738 (mm) REVERT: A 58 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: A 87 TYR cc_start: 0.5128 (m-10) cc_final: 0.4906 (m-10) REVERT: A 452 MET cc_start: 0.0780 (mtm) cc_final: 0.0163 (mmt) REVERT: A 563 MET cc_start: 0.2491 (ttt) cc_final: 0.2175 (ttp) REVERT: A 587 LYS cc_start: 0.6843 (ptmt) cc_final: 0.5539 (tppt) REVERT: A 633 ASP cc_start: 0.8179 (t0) cc_final: 0.6579 (p0) REVERT: A 729 LEU cc_start: 0.4901 (OUTLIER) cc_final: 0.4668 (mp) REVERT: A 773 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 843 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7876 (t0) REVERT: A 913 MET cc_start: 0.7561 (tpt) cc_final: 0.6793 (ptt) REVERT: A 940 ASP cc_start: 0.6063 (m-30) cc_final: 0.5638 (m-30) REVERT: A 970 ILE cc_start: 0.5355 (mm) cc_final: 0.4983 (mm) REVERT: A 993 ASN cc_start: 0.8252 (m-40) cc_final: 0.7740 (p0) REVERT: A 994 GLN cc_start: 0.7459 (mt0) cc_final: 0.7196 (pm20) REVERT: A 1084 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8070 (tt0) REVERT: A 1116 PHE cc_start: 0.5907 (m-80) cc_final: 0.5596 (m-80) REVERT: A 1174 LYS cc_start: 0.4383 (mttt) cc_final: 0.3438 (tptp) REVERT: B 310 TRP cc_start: 0.6006 (m-90) cc_final: 0.5789 (m-90) REVERT: B 473 PHE cc_start: -0.0064 (OUTLIER) cc_final: -0.0747 (t80) REVERT: B 633 ASP cc_start: 0.8077 (m-30) cc_final: 0.7491 (p0) REVERT: B 696 MET cc_start: 0.6246 (mmt) cc_final: 0.5920 (mmm) REVERT: B 821 LEU cc_start: 0.7522 (pp) cc_final: 0.6875 (tp) REVERT: B 843 ASP cc_start: 0.8315 (m-30) cc_final: 0.7994 (t0) REVERT: B 1068 ASP cc_start: 0.8567 (m-30) cc_final: 0.8267 (t0) REVERT: B 1112 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8103 (mppt) REVERT: C 58 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7538 (t80) REVERT: C 161 MET cc_start: -0.1093 (mmt) cc_final: -0.1900 (mmm) REVERT: C 240 MET cc_start: 0.2680 (mtt) cc_final: 0.1356 (mmp) REVERT: C 361 TYR cc_start: 0.7929 (m-80) cc_final: 0.7652 (m-80) REVERT: C 510 ASP cc_start: 0.2178 (OUTLIER) cc_final: 0.1797 (m-30) REVERT: C 563 MET cc_start: 0.1669 (mmm) cc_final: 0.0660 (mtp) REVERT: C 633 ASP cc_start: 0.8092 (m-30) cc_final: 0.6691 (p0) REVERT: C 673 LEU cc_start: 0.7217 (tt) cc_final: 0.6897 (tp) REVERT: C 696 MET cc_start: 0.4661 (mtm) cc_final: 0.4287 (mmm) REVERT: C 978 TYR cc_start: 0.8203 (m-10) cc_final: 0.7916 (m-10) REVERT: C 1098 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8602 (tp) REVERT: C 1174 LYS cc_start: 0.5390 (mttt) cc_final: 0.4497 (tptm) outliers start: 62 outliers final: 51 residues processed: 324 average time/residue: 0.3549 time to fit residues: 190.3960 Evaluate side-chains 332 residues out of total 2946 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 273 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 802 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1106 CYS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.7980 chunk 289 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.0040 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.211684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.186615 restraints weight = 96379.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.190325 restraints weight = 155655.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.191935 restraints weight = 51876.937| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.8998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 27441 Z= 0.322 Angle : 1.105 59.197 37314 Z= 0.607 Chirality : 0.054 1.168 4251 Planarity : 0.006 0.111 4779 Dihedral : 6.638 57.733 4355 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.39 % Favored : 87.40 % Rotamer: Outliers : 2.02 % Allowed : 22.44 % Favored : 75.54 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 3.65 % Twisted Proline : 1.36 % Twisted General : 0.40 % 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: -2.29 (0.14), residues: 3390 helix: 0.42 (0.20), residues: 669 sheet: -0.82 (0.20), residues: 690 loop : -2.60 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 310 HIS 0.007 0.001 HIS A 681 PHE 0.029 0.002 PHE A 116 TYR 0.053 0.002 TYR C 642 ARG 0.007 0.001 ARG A 841 =============================================================================== Job complete usr+sys time: 5667.03 seconds wall clock time: 104 minutes 3.42 seconds (6243.42 seconds total)