Starting phenix.real_space_refine on Sat Mar 16 00:26:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf9_22847/03_2024/7kf9_22847.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 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 42 5.16 5 C 8331 2.51 5 N 2214 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13161 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "B" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1724 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.93, per 1000 atoms: 0.60 Number of scatterers: 13161 At special positions: 0 Unit cell: (148.35, 148.35, 106.95, 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 42 16.00 O 2574 8.00 N 2214 7.00 C 8331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 257 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 257 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 257 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN D 563 " " NAG N 1 " - " ASN F 563 " " NAG O 1 " - " ASN E 563 " Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.3 seconds 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 27 sheets defined 16.8% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.785A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 528 through 532 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.033A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.787A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 528 through 532 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.032A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 3.908A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.217A pdb=" N TYR G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 38 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.755A pdb=" N VAL G 120 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 8.433A pdb=" N ALA A 101 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 65 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLU A 103 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 67 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA7, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA J 10 " --> pdb=" O THR J 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.215A pdb=" N TYR I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP I 36 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.757A pdb=" N VAL I 120 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.259A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.553A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.216A pdb=" N TYR H 35 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP H 36 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.756A pdb=" N VAL H 120 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 45 removed outlier: 5.260A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.583A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.545A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.968A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.613A pdb=" N ALA K 10 " --> pdb=" O THR K 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 17 through 23 516 hydrogen bonds defined for protein. 1263 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: 4.09 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2727 1.32 - 1.46: 4619 1.46 - 1.59: 6025 1.59 - 1.73: 48 1.73 - 1.87: 45 Bond restraints: 13464 Sorted by residual: bond pdb=" CB HIS A 154 " pdb=" CG HIS A 154 " ideal model delta sigma weight residual 1.497 1.383 0.114 1.40e-02 5.10e+03 6.68e+01 bond pdb=" CB HIS B 154 " pdb=" CG HIS B 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.57e+01 bond pdb=" CB HIS C 154 " pdb=" CG HIS C 154 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.47e+01 bond pdb=" CB LEU L 111 " pdb=" CG LEU L 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" CB LEU J 111 " pdb=" CG LEU J 111 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 85.87 - 95.81: 3 95.81 - 105.74: 433 105.74 - 115.67: 8299 115.67 - 125.61: 9250 125.61 - 135.54: 318 Bond angle restraints: 18303 Sorted by residual: angle pdb=" C ALA C 125 " pdb=" N PRO C 126 " pdb=" CA PRO C 126 " ideal model delta sigma weight residual 120.21 128.35 -8.14 9.60e-01 1.09e+00 7.19e+01 angle pdb=" C ALA B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta sigma weight residual 120.21 128.24 -8.03 9.60e-01 1.09e+00 7.00e+01 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.21 128.20 -7.99 9.60e-01 1.09e+00 6.93e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.22 -7.19 9.90e-01 1.02e+00 5.27e+01 angle pdb=" C GLY F 536 " pdb=" N PRO F 537 " pdb=" CA PRO F 537 " ideal model delta sigma weight residual 120.03 127.19 -7.16 9.90e-01 1.02e+00 5.23e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 7926 21.36 - 42.72: 156 42.72 - 64.07: 45 64.07 - 85.43: 33 85.43 - 106.79: 18 Dihedral angle restraints: 8178 sinusoidal: 3474 harmonic: 4704 Sorted by residual: dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.08 106.79 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.01 106.72 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.95 106.66 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 8175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1374 0.097 - 0.194: 515 0.194 - 0.291: 138 0.291 - 0.388: 42 0.388 - 0.484: 22 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 ... (remaining 2088 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 113 " 0.070 2.00e-02 2.50e+03 3.62e-02 2.62e+01 pdb=" CG TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR I 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR I 113 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR I 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 113 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 113 " 0.070 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 113 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR H 113 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 113 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR H 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR H 113 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 113 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 113 " -0.070 2.00e-02 2.50e+03 3.59e-02 2.57e+01 pdb=" CG TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR G 113 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 113 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 113 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 113 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 113 " -0.044 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6637 2.96 - 3.44: 12335 3.44 - 3.93: 23579 3.93 - 4.41: 27520 4.41 - 4.90: 42979 Nonbonded interactions: 113050 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.470 2.520 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.471 2.520 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.471 2.520 nonbonded pdb=" N THR B 249 " pdb=" O THR B 249 " model vdw 2.480 2.496 nonbonded pdb=" N THR C 249 " pdb=" O THR C 249 " model vdw 2.480 2.496 ... (remaining 113045 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.010 Extract box with map and model: 5.580 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.270 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.021 0.148 13464 Z= 1.419 Angle : 1.880 15.027 18303 Z= 1.249 Chirality : 0.117 0.484 2091 Planarity : 0.009 0.053 2313 Dihedral : 12.391 106.789 5169 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1626 helix: -0.35 (0.29), residues: 195 sheet: -0.12 (0.23), residues: 489 loop : 0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.011 TRP H 49 HIS 0.008 0.003 HIS E 549 PHE 0.038 0.006 PHE H 80 TYR 0.070 0.012 TYR I 113 ARG 0.008 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 1.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8740 (ttt) cc_final: 0.7477 (tmm) REVERT: A 171 TYR cc_start: 0.9331 (m-80) cc_final: 0.9011 (m-80) REVERT: A 237 ASP cc_start: 0.9043 (t0) cc_final: 0.8730 (m-30) REVERT: J 35 ASP cc_start: 0.9207 (m-30) cc_final: 0.8372 (p0) REVERT: J 53 ASP cc_start: 0.8865 (p0) cc_final: 0.7836 (t0) REVERT: I 118 MET cc_start: 0.8656 (ttt) cc_final: 0.7637 (tmm) REVERT: C 99 TYR cc_start: 0.7360 (m-80) cc_final: 0.6746 (m-80) REVERT: C 109 TYR cc_start: 0.8670 (m-80) cc_final: 0.8437 (m-10) REVERT: C 237 ASP cc_start: 0.9032 (t0) cc_final: 0.8662 (m-30) REVERT: L 35 ASP cc_start: 0.9168 (m-30) cc_final: 0.8444 (p0) REVERT: L 53 ASP cc_start: 0.8886 (p0) cc_final: 0.7882 (t0) REVERT: H 118 MET cc_start: 0.8807 (ttt) cc_final: 0.7804 (tmm) REVERT: B 127 ASP cc_start: 0.9447 (m-30) cc_final: 0.9213 (t0) REVERT: B 237 ASP cc_start: 0.9006 (t0) cc_final: 0.8606 (m-30) REVERT: K 35 ASP cc_start: 0.9210 (m-30) cc_final: 0.8460 (p0) REVERT: K 53 ASP cc_start: 0.8913 (p0) cc_final: 0.7986 (t0) outliers start: 6 outliers final: 0 residues processed: 227 average time/residue: 0.2831 time to fit residues: 89.4595 Evaluate side-chains 77 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN C 107 ASN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN B 107 ASN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13464 Z= 0.266 Angle : 0.740 7.016 18303 Z= 0.406 Chirality : 0.048 0.250 2091 Planarity : 0.005 0.032 2313 Dihedral : 9.516 74.844 2292 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.78 % Favored : 98.03 % Rotamer: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1626 helix: -0.05 (0.33), residues: 195 sheet: -0.22 (0.19), residues: 636 loop : 0.71 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 100 HIS 0.002 0.001 HIS A 139 PHE 0.030 0.003 PHE A 252 TYR 0.017 0.002 TYR H 113 ARG 0.009 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.502 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8771 (ttt) cc_final: 0.8012 (tmm) REVERT: A 171 TYR cc_start: 0.9121 (m-80) cc_final: 0.8543 (m-80) REVERT: A 237 ASP cc_start: 0.8950 (t0) cc_final: 0.8683 (m-30) REVERT: J 35 ASP cc_start: 0.9118 (m-30) cc_final: 0.8764 (t0) REVERT: J 61 ASP cc_start: 0.9544 (p0) cc_final: 0.9313 (p0) REVERT: I 118 MET cc_start: 0.8661 (ttt) cc_final: 0.8031 (tmm) REVERT: C 122 LEU cc_start: 0.9081 (mt) cc_final: 0.8823 (mt) REVERT: C 171 TYR cc_start: 0.9286 (m-80) cc_final: 0.8942 (m-80) REVERT: C 237 ASP cc_start: 0.8925 (t0) cc_final: 0.8683 (m-30) REVERT: L 35 ASP cc_start: 0.9205 (m-30) cc_final: 0.8965 (t0) REVERT: L 61 ASP cc_start: 0.9521 (p0) cc_final: 0.9304 (p0) REVERT: H 118 MET cc_start: 0.8694 (ttt) cc_final: 0.8002 (tmm) REVERT: B 171 TYR cc_start: 0.9250 (m-80) cc_final: 0.8924 (m-80) REVERT: B 237 ASP cc_start: 0.8895 (t0) cc_final: 0.8550 (m-30) REVERT: K 35 ASP cc_start: 0.9107 (m-30) cc_final: 0.8821 (t0) REVERT: K 61 ASP cc_start: 0.9459 (p0) cc_final: 0.9247 (p0) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.2580 time to fit residues: 50.9969 Evaluate side-chains 70 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 13464 Z= 0.559 Angle : 1.002 11.185 18303 Z= 0.517 Chirality : 0.051 0.384 2091 Planarity : 0.006 0.046 2313 Dihedral : 8.821 55.592 2292 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1626 helix: -0.57 (0.31), residues: 195 sheet: -0.42 (0.20), residues: 627 loop : 0.27 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP I 121 HIS 0.008 0.003 HIS D 516 PHE 0.022 0.003 PHE I 52 TYR 0.025 0.004 TYR A 99 ARG 0.009 0.001 ARG E 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.479 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: G 118 MET cc_start: 0.8392 (ttt) cc_final: 0.8181 (tmm) REVERT: A 171 TYR cc_start: 0.9315 (m-80) cc_final: 0.8680 (m-80) REVERT: A 234 PHE cc_start: 0.8978 (t80) cc_final: 0.8564 (t80) REVERT: A 236 VAL cc_start: 0.8601 (t) cc_final: 0.8347 (t) REVERT: A 237 ASP cc_start: 0.9188 (t0) cc_final: 0.8690 (m-30) REVERT: J 61 ASP cc_start: 0.9491 (p0) cc_final: 0.9268 (p0) REVERT: I 118 MET cc_start: 0.8594 (ttt) cc_final: 0.8366 (tmm) REVERT: C 171 TYR cc_start: 0.9414 (m-80) cc_final: 0.9101 (m-80) REVERT: C 237 ASP cc_start: 0.9183 (t0) cc_final: 0.8576 (m-30) REVERT: H 118 MET cc_start: 0.8473 (ttt) cc_final: 0.8260 (tmm) REVERT: B 122 LEU cc_start: 0.9337 (mt) cc_final: 0.9057 (mt) REVERT: B 171 TYR cc_start: 0.9272 (m-80) cc_final: 0.9056 (m-80) REVERT: B 237 ASP cc_start: 0.9174 (t0) cc_final: 0.8720 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2918 time to fit residues: 35.2711 Evaluate side-chains 57 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13464 Z= 0.264 Angle : 0.686 8.101 18303 Z= 0.354 Chirality : 0.046 0.262 2091 Planarity : 0.004 0.040 2313 Dihedral : 7.491 44.327 2292 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1626 helix: -0.37 (0.32), residues: 195 sheet: -0.48 (0.19), residues: 657 loop : 0.47 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 121 HIS 0.002 0.001 HIS F 516 PHE 0.019 0.002 PHE A 234 TYR 0.012 0.002 TYR A 99 ARG 0.005 0.000 ARG D 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.214 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: symmetry clash REVERT: G 118 MET cc_start: 0.8587 (ttt) cc_final: 0.8077 (tmm) REVERT: A 171 TYR cc_start: 0.9268 (m-80) cc_final: 0.8702 (m-80) REVERT: A 234 PHE cc_start: 0.8981 (t80) cc_final: 0.8646 (t80) REVERT: A 236 VAL cc_start: 0.8641 (t) cc_final: 0.8438 (t) REVERT: A 237 ASP cc_start: 0.9156 (t0) cc_final: 0.8610 (m-30) REVERT: D 517 TYR cc_start: 0.7737 (m-80) cc_final: 0.7421 (m-10) REVERT: J 61 ASP cc_start: 0.9521 (p0) cc_final: 0.9317 (p0) REVERT: I 45 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9276 (tmtt) REVERT: I 118 MET cc_start: 0.8815 (ttt) cc_final: 0.8271 (tmm) REVERT: C 171 TYR cc_start: 0.9284 (m-80) cc_final: 0.8891 (m-80) REVERT: C 234 PHE cc_start: 0.9032 (t80) cc_final: 0.8732 (t80) REVERT: C 237 ASP cc_start: 0.9164 (t0) cc_final: 0.8564 (m-30) REVERT: F 548 MET cc_start: 0.8002 (mmp) cc_final: 0.6220 (mtt) REVERT: H 45 LYS cc_start: 0.9536 (mmtt) cc_final: 0.9286 (tmtt) REVERT: H 118 MET cc_start: 0.8724 (ttt) cc_final: 0.8143 (tmm) REVERT: B 122 LEU cc_start: 0.9278 (mt) cc_final: 0.9039 (mt) REVERT: B 171 TYR cc_start: 0.9235 (m-80) cc_final: 0.8923 (m-80) REVERT: B 234 PHE cc_start: 0.9029 (t80) cc_final: 0.8825 (t80) REVERT: B 237 ASP cc_start: 0.9203 (t0) cc_final: 0.8682 (m-30) REVERT: E 517 TYR cc_start: 0.7651 (m-80) cc_final: 0.7332 (m-10) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2884 time to fit residues: 36.9979 Evaluate side-chains 66 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13464 Z= 0.373 Angle : 0.761 10.108 18303 Z= 0.389 Chirality : 0.047 0.327 2091 Planarity : 0.005 0.054 2313 Dihedral : 6.994 37.597 2292 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1626 helix: -0.44 (0.32), residues: 195 sheet: -0.68 (0.19), residues: 657 loop : 0.24 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 597 HIS 0.004 0.002 HIS D 549 PHE 0.018 0.003 PHE A 234 TYR 0.021 0.002 TYR A 99 ARG 0.003 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.532 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TYR cc_start: 0.9297 (m-80) cc_final: 0.8784 (m-80) REVERT: A 234 PHE cc_start: 0.8995 (t80) cc_final: 0.8712 (t80) REVERT: A 236 VAL cc_start: 0.8739 (t) cc_final: 0.8426 (t) REVERT: A 237 ASP cc_start: 0.9223 (t0) cc_final: 0.8584 (m-30) REVERT: J 61 ASP cc_start: 0.9529 (p0) cc_final: 0.9329 (p0) REVERT: C 171 TYR cc_start: 0.9296 (m-80) cc_final: 0.9031 (m-80) REVERT: C 234 PHE cc_start: 0.9132 (t80) cc_final: 0.8882 (t80) REVERT: C 237 ASP cc_start: 0.9268 (t0) cc_final: 0.8625 (m-30) REVERT: F 548 MET cc_start: 0.8116 (mmp) cc_final: 0.7271 (mmt) REVERT: B 122 LEU cc_start: 0.9286 (mt) cc_final: 0.8989 (mt) REVERT: B 171 TYR cc_start: 0.9243 (m-80) cc_final: 0.8895 (m-80) REVERT: B 237 ASP cc_start: 0.9198 (t0) cc_final: 0.8594 (m-30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2785 time to fit residues: 33.1922 Evaluate side-chains 57 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 GLN J 38 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13464 Z= 0.170 Angle : 0.597 7.721 18303 Z= 0.308 Chirality : 0.045 0.231 2091 Planarity : 0.004 0.045 2313 Dihedral : 6.143 31.660 2292 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1626 helix: -0.04 (0.35), residues: 198 sheet: -0.51 (0.20), residues: 633 loop : 0.40 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 275 HIS 0.002 0.001 HIS D 516 PHE 0.018 0.002 PHE A 234 TYR 0.010 0.002 TYR H 96 ARG 0.002 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.308 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8708 (ttt) cc_final: 0.8132 (tmm) REVERT: A 171 TYR cc_start: 0.9207 (m-80) cc_final: 0.8630 (m-80) REVERT: A 234 PHE cc_start: 0.8990 (t80) cc_final: 0.8755 (t80) REVERT: A 237 ASP cc_start: 0.9246 (t0) cc_final: 0.8586 (m-30) REVERT: I 118 MET cc_start: 0.8674 (ttt) cc_final: 0.8180 (tmm) REVERT: C 171 TYR cc_start: 0.9253 (m-80) cc_final: 0.8857 (m-80) REVERT: C 234 PHE cc_start: 0.9094 (t80) cc_final: 0.8866 (t80) REVERT: C 237 ASP cc_start: 0.9271 (t0) cc_final: 0.8587 (m-30) REVERT: F 545 GLU cc_start: 0.9160 (pm20) cc_final: 0.8919 (pp20) REVERT: F 548 MET cc_start: 0.8098 (mmp) cc_final: 0.7859 (mmt) REVERT: H 118 MET cc_start: 0.8748 (ttt) cc_final: 0.8108 (tmm) REVERT: B 33 ILE cc_start: 0.9049 (tp) cc_final: 0.8062 (tp) REVERT: B 122 LEU cc_start: 0.9251 (mt) cc_final: 0.9023 (mt) REVERT: B 171 TYR cc_start: 0.9210 (m-80) cc_final: 0.8876 (m-10) REVERT: B 234 PHE cc_start: 0.9133 (t80) cc_final: 0.8917 (t80) REVERT: B 237 ASP cc_start: 0.9201 (t0) cc_final: 0.8543 (m-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3085 time to fit residues: 43.0657 Evaluate side-chains 66 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 89 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 0.0070 chunk 98 optimal weight: 8.9990 overall best weight: 4.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 38 GLN ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13464 Z= 0.303 Angle : 0.676 9.626 18303 Z= 0.347 Chirality : 0.046 0.359 2091 Planarity : 0.006 0.151 2313 Dihedral : 6.201 28.857 2292 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1626 helix: -0.01 (0.35), residues: 195 sheet: -0.53 (0.20), residues: 633 loop : 0.28 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 275 HIS 0.003 0.001 HIS A 139 PHE 0.015 0.002 PHE A 234 TYR 0.016 0.002 TYR C 241 ARG 0.014 0.001 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.451 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: symmetry clash REVERT: G 104 ARG cc_start: 0.5037 (mpt-90) cc_final: 0.4657 (mmt90) REVERT: G 118 MET cc_start: 0.8739 (ttt) cc_final: 0.8117 (tmm) REVERT: A 171 TYR cc_start: 0.9299 (m-80) cc_final: 0.8720 (m-80) REVERT: A 234 PHE cc_start: 0.9011 (t80) cc_final: 0.8805 (t80) REVERT: A 237 ASP cc_start: 0.9347 (t0) cc_final: 0.8652 (m-30) REVERT: D 548 MET cc_start: 0.7604 (mpp) cc_final: 0.6948 (mtp) REVERT: I 104 ARG cc_start: 0.4711 (mpt-90) cc_final: 0.4296 (mmt90) REVERT: I 118 MET cc_start: 0.8681 (ttt) cc_final: 0.8208 (tmm) REVERT: C 171 TYR cc_start: 0.9281 (m-80) cc_final: 0.8966 (m-80) REVERT: C 234 PHE cc_start: 0.9142 (t80) cc_final: 0.8910 (t80) REVERT: C 237 ASP cc_start: 0.9391 (t0) cc_final: 0.8674 (m-30) REVERT: F 548 MET cc_start: 0.8078 (mmp) cc_final: 0.7573 (mmt) REVERT: H 118 MET cc_start: 0.8728 (ttt) cc_final: 0.8175 (tmm) REVERT: B 122 LEU cc_start: 0.9286 (mt) cc_final: 0.9002 (mt) REVERT: B 171 TYR cc_start: 0.9258 (m-80) cc_final: 0.8935 (m-80) REVERT: B 237 ASP cc_start: 0.9335 (t0) cc_final: 0.8614 (m-30) REVERT: E 548 MET cc_start: 0.7891 (mpp) cc_final: 0.7075 (mtp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2923 time to fit residues: 36.3945 Evaluate side-chains 67 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13464 Z= 0.241 Angle : 0.629 8.206 18303 Z= 0.325 Chirality : 0.045 0.307 2091 Planarity : 0.006 0.128 2313 Dihedral : 6.058 25.592 2292 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1626 helix: 0.02 (0.36), residues: 198 sheet: -0.45 (0.20), residues: 603 loop : 0.23 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 275 HIS 0.003 0.001 HIS D 516 PHE 0.019 0.002 PHE B 234 TYR 0.016 0.002 TYR A 99 ARG 0.006 0.000 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.531 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 118 MET cc_start: 0.8708 (ttt) cc_final: 0.8140 (tmm) REVERT: A 171 TYR cc_start: 0.9243 (m-80) cc_final: 0.8633 (m-80) REVERT: A 234 PHE cc_start: 0.9036 (t80) cc_final: 0.8828 (t80) REVERT: A 237 ASP cc_start: 0.9359 (t0) cc_final: 0.8605 (m-30) REVERT: I 118 MET cc_start: 0.8675 (ttt) cc_final: 0.8196 (tmm) REVERT: C 171 TYR cc_start: 0.9320 (m-80) cc_final: 0.8939 (m-80) REVERT: C 234 PHE cc_start: 0.9147 (t80) cc_final: 0.8930 (t80) REVERT: C 237 ASP cc_start: 0.9357 (t0) cc_final: 0.8594 (m-30) REVERT: F 504 ILE cc_start: 0.5598 (mp) cc_final: 0.5359 (mp) REVERT: F 548 MET cc_start: 0.8044 (mmp) cc_final: 0.7600 (mmt) REVERT: H 118 MET cc_start: 0.8807 (ttt) cc_final: 0.8276 (tmm) REVERT: B 122 LEU cc_start: 0.9262 (mt) cc_final: 0.9055 (mt) REVERT: B 171 TYR cc_start: 0.9237 (m-80) cc_final: 0.8892 (m-80) REVERT: B 234 PHE cc_start: 0.8997 (t80) cc_final: 0.8795 (t80) REVERT: B 237 ASP cc_start: 0.9290 (t0) cc_final: 0.8535 (m-30) REVERT: E 548 MET cc_start: 0.7715 (mpp) cc_final: 0.7142 (mtp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2953 time to fit residues: 38.5159 Evaluate side-chains 67 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 0.0060 chunk 97 optimal weight: 2.9990 overall best weight: 3.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13464 Z= 0.241 Angle : 0.633 9.739 18303 Z= 0.327 Chirality : 0.045 0.322 2091 Planarity : 0.005 0.123 2313 Dihedral : 5.908 28.041 2292 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1626 helix: 0.09 (0.36), residues: 195 sheet: -0.56 (0.20), residues: 633 loop : 0.30 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 531 HIS 0.007 0.001 HIS L 99 PHE 0.021 0.002 PHE B 234 TYR 0.012 0.002 TYR F 517 ARG 0.004 0.000 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.532 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 ARG cc_start: 0.4613 (mpt-90) cc_final: 0.4175 (mmt90) REVERT: G 118 MET cc_start: 0.8733 (ttt) cc_final: 0.8161 (tmm) REVERT: A 161 LEU cc_start: 0.9444 (mt) cc_final: 0.9185 (mt) REVERT: A 171 TYR cc_start: 0.9277 (m-80) cc_final: 0.8677 (m-80) REVERT: A 234 PHE cc_start: 0.9034 (t80) cc_final: 0.8833 (t80) REVERT: A 237 ASP cc_start: 0.9364 (t0) cc_final: 0.8601 (m-30) REVERT: I 104 ARG cc_start: 0.4357 (mpt-90) cc_final: 0.4052 (mmt90) REVERT: I 118 MET cc_start: 0.8598 (ttt) cc_final: 0.8102 (tmm) REVERT: C 161 LEU cc_start: 0.9533 (mt) cc_final: 0.9332 (mt) REVERT: C 171 TYR cc_start: 0.9333 (m-80) cc_final: 0.8957 (m-80) REVERT: C 234 PHE cc_start: 0.9138 (t80) cc_final: 0.8925 (t80) REVERT: C 237 ASP cc_start: 0.9327 (t0) cc_final: 0.8664 (m-30) REVERT: F 548 MET cc_start: 0.8037 (mmp) cc_final: 0.7792 (mmt) REVERT: H 118 MET cc_start: 0.8794 (ttt) cc_final: 0.8233 (tmm) REVERT: B 171 TYR cc_start: 0.9245 (m-80) cc_final: 0.8969 (m-80) REVERT: B 234 PHE cc_start: 0.9022 (t80) cc_final: 0.8791 (t80) REVERT: B 237 ASP cc_start: 0.9280 (t0) cc_final: 0.8547 (m-30) REVERT: E 531 TRP cc_start: 0.7259 (m100) cc_final: 0.6704 (m-10) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2778 time to fit residues: 37.6270 Evaluate side-chains 68 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 0.0020 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 101 optimal weight: 0.0050 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.0204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13464 Z= 0.153 Angle : 0.589 9.211 18303 Z= 0.301 Chirality : 0.044 0.233 2091 Planarity : 0.005 0.104 2313 Dihedral : 5.510 27.715 2292 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1626 helix: 0.16 (0.36), residues: 195 sheet: -0.49 (0.20), residues: 633 loop : 0.47 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 531 HIS 0.007 0.001 HIS E 549 PHE 0.022 0.002 PHE B 234 TYR 0.017 0.001 TYR E 517 ARG 0.004 0.000 ARG B 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3252 Ramachandran restraints generated. 1626 Oldfield, 0 Emsley, 1626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.297 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 ARG cc_start: 0.4241 (mpt-90) cc_final: 0.3867 (mmt90) REVERT: G 118 MET cc_start: 0.8716 (ttt) cc_final: 0.8184 (tmm) REVERT: A 171 TYR cc_start: 0.9259 (m-80) cc_final: 0.8652 (m-80) REVERT: A 234 PHE cc_start: 0.9030 (t80) cc_final: 0.8806 (t80) REVERT: A 237 ASP cc_start: 0.9358 (t0) cc_final: 0.8805 (m-30) REVERT: I 104 ARG cc_start: 0.4072 (mpt-90) cc_final: 0.3870 (mmt90) REVERT: I 118 MET cc_start: 0.8669 (ttt) cc_final: 0.8205 (tmm) REVERT: C 161 LEU cc_start: 0.9594 (mt) cc_final: 0.9389 (mt) REVERT: C 171 TYR cc_start: 0.9297 (m-80) cc_final: 0.8818 (m-80) REVERT: C 234 PHE cc_start: 0.9085 (t80) cc_final: 0.8865 (t80) REVERT: C 237 ASP cc_start: 0.9467 (t0) cc_final: 0.8647 (m-30) REVERT: F 548 MET cc_start: 0.8038 (mmp) cc_final: 0.7810 (mmt) REVERT: H 118 MET cc_start: 0.8816 (ttt) cc_final: 0.8253 (tmm) REVERT: B 171 TYR cc_start: 0.9245 (m-80) cc_final: 0.8894 (m-80) REVERT: B 234 PHE cc_start: 0.9026 (t80) cc_final: 0.8778 (t80) REVERT: B 237 ASP cc_start: 0.9252 (t0) cc_final: 0.8674 (m-30) REVERT: E 531 TRP cc_start: 0.7193 (m100) cc_final: 0.6692 (m-10) REVERT: E 548 MET cc_start: 0.7798 (mpp) cc_final: 0.7114 (mtp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2854 time to fit residues: 39.8113 Evaluate side-chains 71 residues out of total 1395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.027787 restraints weight = 157429.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.028777 restraints weight = 88596.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029508 restraints weight = 59227.316| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13464 Z= 0.258 Angle : 0.636 9.519 18303 Z= 0.325 Chirality : 0.044 0.276 2091 Planarity : 0.005 0.116 2313 Dihedral : 5.601 29.512 2292 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1626 helix: 0.13 (0.37), residues: 198 sheet: -0.40 (0.20), residues: 603 loop : 0.24 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 531 HIS 0.011 0.002 HIS D 516 PHE 0.023 0.002 PHE B 234 TYR 0.015 0.002 TYR E 517 ARG 0.004 0.000 ARG B 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.76 seconds wall clock time: 40 minutes 26.49 seconds (2426.49 seconds total)