Starting phenix.real_space_refine on Thu Mar 21 20:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlz_7959/03_2024/6dlz_7959_updated.pdb" } resolution = 3.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 19996 2.51 5 N 5129 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1203": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1203": "NH1" <-> "NH2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 1005": "NH1" <-> "NH2" Residue "D TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31070 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7730 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 957} Chain breaks: 4 Chain: "B" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7734 Classifications: {'peptide': 984} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 958} Chain breaks: 4 Chain: "D" Number of atoms: 7735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7735 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 21, 'TRANS': 958} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 15.23, per 1000 atoms: 0.49 Number of scatterers: 31070 At special positions: 0 Unit cell: (115.56, 167.4, 199.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5769 8.00 N 5129 7.00 C 19996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.04 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 Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 5.4 seconds 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 133 helices and 32 sheets defined 42.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 36 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.691A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.585A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.940A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.674A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.542A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 removed outlier: 3.502A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.527A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.784A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 removed outlier: 4.324A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.219A pdb=" N GLU A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP A 638 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.922A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 removed outlier: 3.641A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1027 Processing helix chain 'A' and resid 1092 through 1094 No H-bonds generated for 'chain 'A' and resid 1092 through 1094' Processing helix chain 'A' and resid 1096 through 1101 Processing helix chain 'A' and resid 1106 through 1124 removed outlier: 3.804A pdb=" N SER A1110 " --> pdb=" O PHE A1106 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A1111 " --> pdb=" O PRO A1107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1159 removed outlier: 3.564A pdb=" N ALA A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.970A pdb=" N VAL A1194 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1196 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A1202 " --> pdb=" O MET A1199 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A1204 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1206 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.902A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.713A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.584A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.829A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.615A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.842A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.575A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 520 Proline residue: B 520 - end of helix No H-bonds generated for 'chain 'B' and resid 517 through 520' Processing helix chain 'B' and resid 523 through 543 Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.768A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 618 removed outlier: 4.484A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 638 through 641 No H-bonds generated for 'chain 'B' and resid 638 through 641' Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.548A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 743 through 755 removed outlier: 4.130A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.846A pdb=" N SER B 778 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY B 779 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 780 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 818 Processing helix chain 'B' and resid 1008 through 1027 removed outlier: 3.628A pdb=" N LEU B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1088 No H-bonds generated for 'chain 'B' and resid 1086 through 1088' Processing helix chain 'B' and resid 1092 through 1102 Processing helix chain 'B' and resid 1105 through 1122 Processing helix chain 'B' and resid 1133 through 1159 removed outlier: 4.161A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.784A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.694A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.581A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.943A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.673A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.557A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.839A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.516A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.788A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 623 removed outlier: 4.322A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 641 removed outlier: 4.198A pdb=" N GLU C 637 " --> pdb=" O GLU C 634 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP C 638 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.955A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 793 through 819 removed outlier: 3.636A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1027 Processing helix chain 'C' and resid 1092 through 1094 No H-bonds generated for 'chain 'C' and resid 1092 through 1094' Processing helix chain 'C' and resid 1096 through 1101 Processing helix chain 'C' and resid 1106 through 1124 removed outlier: 3.792A pdb=" N SER C1110 " --> pdb=" O PHE C1106 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C1112 " --> pdb=" O ILE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1159 removed outlier: 3.563A pdb=" N ALA C1137 " --> pdb=" O ILE C1133 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C1138 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1208 removed outlier: 3.967A pdb=" N VAL C1194 " --> pdb=" O MET C1191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C1196 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C1202 " --> pdb=" O MET C1199 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C1204 " --> pdb=" O ILE C1201 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C1206 " --> pdb=" O ARG C1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.907A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.711A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.584A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 198 through 211 removed outlier: 3.819A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.600A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.834A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.552A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 543 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.768A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 618 removed outlier: 4.485A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 623 Processing helix chain 'D' and resid 638 through 641 No H-bonds generated for 'chain 'D' and resid 638 through 641' Processing helix chain 'D' and resid 654 through 661 removed outlier: 3.539A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 743 through 755 removed outlier: 4.111A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 774 through 780 removed outlier: 3.842A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 780 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 818 Processing helix chain 'D' and resid 1008 through 1027 removed outlier: 3.630A pdb=" N LEU D1022 " --> pdb=" O ALA D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1088 No H-bonds generated for 'chain 'D' and resid 1086 through 1088' Processing helix chain 'D' and resid 1092 through 1102 Processing helix chain 'D' and resid 1105 through 1122 Processing helix chain 'D' and resid 1133 through 1159 removed outlier: 4.165A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D1154 " --> pdb=" O ILE D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.792A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS D1198 " --> pdb=" O VAL D1194 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 49 Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.101A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 394 through 399 removed outlier: 7.004A pdb=" N LYS A 439 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A 397 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= F, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.955A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.419A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.497A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 72 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU B 17 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 74 " --> pdb=" O LEU B 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.250A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= N, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.954A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.425A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 1033 through 1036 removed outlier: 3.598A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 42 through 49 Processing sheet with id= R, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= S, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.100A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.996A pdb=" N LYS C 439 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL C 397 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= V, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.946A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.421A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.576A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.490A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA D 72 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU D 17 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE D 74 " --> pdb=" O LEU D 17 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= AA, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.248A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AC, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AD, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.981A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.431A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 1033 through 1036 removed outlier: 3.602A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1196 hydrogen bonds defined for protein. 3396 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: 9.89 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 550 1.23 - 1.38: 11838 1.38 - 1.53: 18308 1.53 - 1.69: 766 1.69 - 1.84: 280 Bond restraints: 31742 Sorted by residual: bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.079 0.433 2.00e-02 2.50e+03 4.68e+02 bond pdb=" C4 CYZ D1302 " pdb=" C5 CYZ D1302 " ideal model delta sigma weight residual 1.512 1.080 0.432 2.00e-02 2.50e+03 4.67e+02 bond pdb=" C4 CYZ A1302 " pdb=" C5 CYZ A1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " ideal model delta sigma weight residual 1.512 1.081 0.431 2.00e-02 2.50e+03 4.65e+02 bond pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " ideal model delta sigma weight residual 1.557 1.126 0.431 2.00e-02 2.50e+03 4.63e+02 ... (remaining 31737 not shown) Histogram of bond angle deviations from ideal: 87.25 - 97.39: 20 97.39 - 107.53: 1015 107.53 - 117.66: 22176 117.66 - 127.80: 19437 127.80 - 137.94: 251 Bond angle restraints: 42899 Sorted by residual: angle pdb=" C1 CYZ D1302 " pdb=" C2 CYZ D1302 " pdb=" C3 CYZ D1302 " ideal model delta sigma weight residual 106.92 137.94 -31.02 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 137.80 -30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C1 CYZ C1302 " pdb=" C2 CYZ C1302 " pdb=" C3 CYZ C1302 " ideal model delta sigma weight residual 106.92 137.71 -30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C3 CYZ A1302 " ideal model delta sigma weight residual 106.92 137.65 -30.73 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C4 CYZ C1302 " pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 105.93 132.25 -26.32 3.00e+00 1.11e-01 7.70e+01 ... (remaining 42894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.06: 18332 24.06 - 48.12: 443 48.12 - 72.18: 16 72.18 - 96.23: 16 96.23 - 120.29: 8 Dihedral angle restraints: 18815 sinusoidal: 7494 harmonic: 11321 Sorted by residual: dihedral pdb=" CA SER D 635 " pdb=" C SER D 635 " pdb=" N ALA D 636 " pdb=" CA ALA D 636 " ideal model delta harmonic sigma weight residual -180.00 -124.91 -55.09 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -125.16 -54.84 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA PRO C 632 " pdb=" C PRO C 632 " pdb=" N ILE C 633 " pdb=" CA ILE C 633 " ideal model delta harmonic sigma weight residual -180.00 -135.62 -44.38 0 5.00e+00 4.00e-02 7.88e+01 ... (remaining 18812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.436: 4748 0.436 - 0.872: 6 0.872 - 1.308: 0 1.308 - 1.744: 0 1.744 - 2.179: 8 Chirality restraints: 4762 Sorted by residual: chirality pdb=" C5 CYZ B1302 " pdb=" C4 CYZ B1302 " pdb=" C6 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ D1302 " pdb=" C4 CYZ D1302 " pdb=" C6 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.19e+02 chirality pdb=" C5 CYZ C1302 " pdb=" C4 CYZ C1302 " pdb=" C6 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 1.13 2.18 2.00e-01 2.50e+01 1.18e+02 ... (remaining 4759 not shown) Planarity restraints: 5383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 99 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.061 5.00e-02 4.00e+02 9.27e-02 1.37e+01 pdb=" N PRO A 99 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 99 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.043 5.00e-02 4.00e+02 ... (remaining 5380 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1660 2.72 - 3.26: 30768 3.26 - 3.81: 49894 3.81 - 4.35: 57459 4.35 - 4.90: 96459 Nonbonded interactions: 236240 Sorted by model distance: nonbonded pdb=" O ILE C1025 " pdb=" OG1 THR C1029 " model vdw 2.171 2.440 nonbonded pdb=" O ILE A1025 " pdb=" OG1 THR A1029 " model vdw 2.212 2.440 nonbonded pdb=" O ALA D1026 " pdb=" OG SER D1178 " model vdw 2.228 2.440 nonbonded pdb=" O ALA B1026 " pdb=" OG SER B1178 " model vdw 2.231 2.440 nonbonded pdb=" O GLU B 637 " pdb=" OG SER B 640 " model vdw 2.236 2.440 ... (remaining 236235 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 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1208 or resid 1301 through 1302)) selection = (chain 'B' and (resid 10 through 549 or resid 565 through 1208 or resid 1301 thr \ ough 1302)) selection = (chain 'C' and (resid 10 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 817 or (resid 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 or resid 1002 \ through 1208 or resid 1301 through 1302)) selection = (chain 'D' and (resid 10 through 549 or resid 565 through 1208 or resid 1301 thr \ ough 1302)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.260 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 74.090 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.160 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.013 0.433 31742 Z= 0.842 Angle : 1.190 31.018 42899 Z= 0.641 Chirality : 0.104 2.179 4762 Planarity : 0.007 0.093 5383 Dihedral : 10.995 120.293 11539 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.47 % Favored : 91.12 % Rotamer: Outliers : 0.60 % Allowed : 3.93 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.78 (0.11), residues: 3897 helix: -1.98 (0.09), residues: 1788 sheet: -2.05 (0.24), residues: 410 loop : -3.17 (0.12), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 578 HIS 0.011 0.002 HIS D 93 PHE 0.023 0.003 PHE C1106 TYR 0.024 0.003 TYR A1031 ARG 0.008 0.001 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 510 time to evaluate : 3.468 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: A 369 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7391 (ttm-80) REVERT: A 408 MET cc_start: 0.8965 (mmm) cc_final: 0.8195 (tpp) REVERT: A 427 ASP cc_start: 0.8453 (m-30) cc_final: 0.8140 (m-30) REVERT: A 670 MET cc_start: 0.9215 (mtp) cc_final: 0.8937 (mtt) REVERT: A 728 ASP cc_start: 0.8165 (p0) cc_final: 0.7934 (m-30) REVERT: A 1104 SER cc_start: 0.8331 (p) cc_final: 0.7459 (t) REVERT: A 1113 LEU cc_start: 0.9072 (mt) cc_final: 0.8806 (mt) REVERT: A 1127 TYR cc_start: 0.8354 (t80) cc_final: 0.8000 (t80) REVERT: A 1140 PHE cc_start: 0.9027 (m-80) cc_final: 0.8566 (m-80) REVERT: A 1170 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8308 (pttp) REVERT: A 1188 ILE cc_start: 0.9365 (mm) cc_final: 0.9088 (tp) REVERT: B 113 MET cc_start: 0.8793 (mmp) cc_final: 0.8046 (mpp) REVERT: B 504 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 710 GLU cc_start: 0.8665 (pt0) cc_final: 0.8044 (pp20) REVERT: B 748 LEU cc_start: 0.9450 (mt) cc_final: 0.9246 (mm) REVERT: B 1009 MET cc_start: 0.8527 (tpt) cc_final: 0.8258 (tpp) REVERT: B 1116 MET cc_start: 0.9036 (tpp) cc_final: 0.8813 (tpp) REVERT: B 1180 TYR cc_start: 0.9290 (m-10) cc_final: 0.8997 (m-80) REVERT: B 1191 MET cc_start: 0.9065 (ttm) cc_final: 0.8752 (tpp) REVERT: B 1199 MET cc_start: 0.9234 (mmm) cc_final: 0.8806 (mmm) REVERT: C 369 ARG cc_start: 0.7646 (ptm160) cc_final: 0.7314 (ttm-80) REVERT: C 408 MET cc_start: 0.8968 (mmm) cc_final: 0.8172 (tpp) REVERT: C 427 ASP cc_start: 0.8443 (m-30) cc_final: 0.8140 (m-30) REVERT: C 670 MET cc_start: 0.9223 (mtp) cc_final: 0.8972 (mtt) REVERT: C 728 ASP cc_start: 0.8153 (p0) cc_final: 0.7903 (m-30) REVERT: C 1104 SER cc_start: 0.8373 (p) cc_final: 0.7447 (t) REVERT: C 1113 LEU cc_start: 0.9076 (mt) cc_final: 0.8804 (mt) REVERT: C 1140 PHE cc_start: 0.9014 (m-80) cc_final: 0.8536 (m-80) REVERT: C 1170 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8207 (pttp) REVERT: C 1188 ILE cc_start: 0.9363 (mm) cc_final: 0.9027 (tt) REVERT: D 113 MET cc_start: 0.8792 (mmp) cc_final: 0.8007 (mpp) REVERT: D 504 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7792 (tt) REVERT: D 519 ASP cc_start: 0.8918 (t70) cc_final: 0.7939 (t70) REVERT: D 623 PHE cc_start: 0.8970 (m-80) cc_final: 0.8427 (m-80) REVERT: D 710 GLU cc_start: 0.8671 (pt0) cc_final: 0.8044 (pp20) REVERT: D 748 LEU cc_start: 0.9457 (mt) cc_final: 0.9247 (mm) REVERT: D 1023 MET cc_start: 0.8989 (tpt) cc_final: 0.8730 (tpp) REVERT: D 1116 MET cc_start: 0.9019 (tpp) cc_final: 0.8809 (tpp) REVERT: D 1180 TYR cc_start: 0.9259 (m-10) cc_final: 0.8931 (m-80) REVERT: D 1191 MET cc_start: 0.9063 (ttm) cc_final: 0.8757 (tpp) outliers start: 20 outliers final: 2 residues processed: 526 average time/residue: 0.4375 time to fit residues: 359.4507 Evaluate side-chains 257 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 253 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain D residue 504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 8.9990 chunk 297 optimal weight: 0.0020 chunk 164 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 158 optimal weight: 0.0870 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 228 optimal weight: 0.0970 chunk 355 optimal weight: 5.9990 overall best weight: 1.8368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 214 HIS A 355 ASN B 24 GLN B 147 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 586 GLN B 642 GLN B 747 ASN B 791 ASN C 147 GLN C 214 HIS C 355 ASN D 24 GLN D 147 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 586 GLN D 642 GLN D 747 ASN D 791 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31742 Z= 0.209 Angle : 0.614 9.986 42899 Z= 0.322 Chirality : 0.041 0.306 4762 Planarity : 0.005 0.071 5383 Dihedral : 7.856 100.655 4385 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 1.86 % Allowed : 9.79 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3897 helix: 0.22 (0.12), residues: 1766 sheet: -1.93 (0.24), residues: 406 loop : -2.75 (0.13), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1032 HIS 0.004 0.001 HIS D 93 PHE 0.017 0.001 PHE C 541 TYR 0.019 0.001 TYR A 523 ARG 0.008 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 300 time to evaluate : 3.578 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: A 380 MET cc_start: 0.7629 (ttt) cc_final: 0.7364 (tmm) REVERT: A 408 MET cc_start: 0.8791 (mmm) cc_final: 0.8384 (tpp) REVERT: A 414 MET cc_start: 0.8801 (mpp) cc_final: 0.8029 (tpp) REVERT: A 670 MET cc_start: 0.9201 (mtp) cc_final: 0.8979 (mtt) REVERT: A 728 ASP cc_start: 0.8048 (p0) cc_final: 0.7648 (m-30) REVERT: A 1113 LEU cc_start: 0.9010 (mt) cc_final: 0.8706 (mt) REVERT: A 1140 PHE cc_start: 0.9042 (m-80) cc_final: 0.8593 (m-80) REVERT: B 463 MET cc_start: 0.8980 (mtp) cc_final: 0.8661 (mmt) REVERT: B 710 GLU cc_start: 0.8713 (pt0) cc_final: 0.8116 (pp20) REVERT: B 1180 TYR cc_start: 0.9195 (m-10) cc_final: 0.8912 (m-80) REVERT: B 1191 MET cc_start: 0.9124 (ttm) cc_final: 0.8851 (tpp) REVERT: C 369 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7293 (ttm-80) REVERT: C 380 MET cc_start: 0.7622 (ttt) cc_final: 0.7357 (tmm) REVERT: C 408 MET cc_start: 0.8774 (mmm) cc_final: 0.8366 (tpp) REVERT: C 414 MET cc_start: 0.8761 (mpp) cc_final: 0.7987 (tmm) REVERT: C 427 ASP cc_start: 0.8660 (m-30) cc_final: 0.8352 (m-30) REVERT: C 728 ASP cc_start: 0.8051 (p0) cc_final: 0.7629 (m-30) REVERT: C 1113 LEU cc_start: 0.9017 (mt) cc_final: 0.8734 (mt) REVERT: C 1127 TYR cc_start: 0.8167 (t80) cc_final: 0.7950 (t80) REVERT: C 1140 PHE cc_start: 0.9041 (m-80) cc_final: 0.8589 (m-80) REVERT: D 463 MET cc_start: 0.8949 (mtp) cc_final: 0.8670 (mmt) REVERT: D 710 GLU cc_start: 0.8706 (pt0) cc_final: 0.8125 (pp20) REVERT: D 1180 TYR cc_start: 0.9205 (m-10) cc_final: 0.8907 (m-80) REVERT: D 1191 MET cc_start: 0.9145 (ttm) cc_final: 0.8874 (tpp) outliers start: 62 outliers final: 34 residues processed: 341 average time/residue: 0.4574 time to fit residues: 253.0479 Evaluate side-chains 281 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 0.8980 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31742 Z= 0.193 Angle : 0.584 10.868 42899 Z= 0.302 Chirality : 0.040 0.264 4762 Planarity : 0.004 0.065 5383 Dihedral : 7.073 85.764 4381 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.88 % Favored : 92.92 % Rotamer: Outliers : 2.61 % Allowed : 10.72 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3897 helix: 1.17 (0.13), residues: 1746 sheet: -1.60 (0.24), residues: 432 loop : -2.57 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1032 HIS 0.003 0.001 HIS C 46 PHE 0.018 0.001 PHE D1096 TYR 0.018 0.001 TYR D 673 ARG 0.006 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 268 time to evaluate : 3.776 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: A 113 MET cc_start: 0.9207 (mmt) cc_final: 0.8636 (mmm) REVERT: A 369 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7483 (ttm-80) REVERT: A 407 MET cc_start: 0.8391 (mtm) cc_final: 0.8188 (mpp) REVERT: A 414 MET cc_start: 0.8801 (mpp) cc_final: 0.7944 (tpp) REVERT: A 728 ASP cc_start: 0.8155 (p0) cc_final: 0.7832 (m-30) REVERT: A 1140 PHE cc_start: 0.8996 (m-80) cc_final: 0.8540 (m-80) REVERT: A 1190 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8983 (mp0) REVERT: B 390 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.3643 (mm) REVERT: B 498 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9340 (pp) REVERT: B 573 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9289 (mt) REVERT: B 710 GLU cc_start: 0.8623 (pt0) cc_final: 0.8053 (pp20) REVERT: B 1180 TYR cc_start: 0.9207 (m-10) cc_final: 0.8989 (m-80) REVERT: C 113 MET cc_start: 0.9209 (mmt) cc_final: 0.8664 (mmm) REVERT: C 369 ARG cc_start: 0.7724 (ptm160) cc_final: 0.7361 (ttm-80) REVERT: C 1140 PHE cc_start: 0.9019 (m-80) cc_final: 0.8535 (m-80) REVERT: C 1190 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8965 (mp0) REVERT: C 1191 MET cc_start: 0.9376 (mpp) cc_final: 0.9094 (mpp) REVERT: D 390 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.3548 (mm) REVERT: D 463 MET cc_start: 0.8940 (mtp) cc_final: 0.8731 (mmt) REVERT: D 498 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9329 (pp) REVERT: D 573 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9287 (mt) REVERT: D 710 GLU cc_start: 0.8638 (pt0) cc_final: 0.8026 (pp20) REVERT: D 1180 TYR cc_start: 0.9201 (m-10) cc_final: 0.8997 (m-80) outliers start: 87 outliers final: 46 residues processed: 328 average time/residue: 0.3840 time to fit residues: 208.4832 Evaluate side-chains 282 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 185 optimal weight: 0.0870 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 378 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 246 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1198 HIS D 246 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31742 Z= 0.146 Angle : 0.550 11.704 42899 Z= 0.278 Chirality : 0.040 0.214 4762 Planarity : 0.004 0.060 5383 Dihedral : 6.060 69.230 4381 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.05 % Rotamer: Outliers : 2.28 % Allowed : 12.13 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.64 (0.14), residues: 3897 helix: 1.58 (0.13), residues: 1750 sheet: -1.31 (0.24), residues: 432 loop : -2.45 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1177 HIS 0.003 0.001 HIS C1059 PHE 0.017 0.001 PHE A 541 TYR 0.021 0.001 TYR D1031 ARG 0.003 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 267 time to evaluate : 3.616 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: A 113 MET cc_start: 0.9153 (mmt) cc_final: 0.8513 (mmm) REVERT: A 369 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: A 414 MET cc_start: 0.8774 (mpp) cc_final: 0.7941 (tpp) REVERT: A 728 ASP cc_start: 0.8142 (p0) cc_final: 0.7776 (m-30) REVERT: A 789 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9161 (tt) REVERT: A 1009 MET cc_start: 0.8995 (tpp) cc_final: 0.8295 (mpp) REVERT: A 1126 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8840 (t80) REVERT: A 1140 PHE cc_start: 0.8973 (m-80) cc_final: 0.8508 (m-80) REVERT: A 1190 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8977 (mp0) REVERT: A 1199 MET cc_start: 0.9417 (tpp) cc_final: 0.9170 (tpp) REVERT: B 390 LEU cc_start: 0.4350 (OUTLIER) cc_final: 0.3589 (mm) REVERT: B 503 MET cc_start: 0.8093 (tmm) cc_final: 0.7782 (tmm) REVERT: B 704 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8517 (pt) REVERT: B 710 GLU cc_start: 0.8614 (pt0) cc_final: 0.8110 (tm-30) REVERT: B 721 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7787 (mpp) REVERT: B 1069 GLU cc_start: 0.8646 (tp30) cc_final: 0.8249 (tt0) REVERT: B 1078 GLN cc_start: 0.7939 (tp40) cc_final: 0.7601 (tp40) REVERT: C 113 MET cc_start: 0.9172 (mmt) cc_final: 0.8549 (mmm) REVERT: C 369 ARG cc_start: 0.7703 (ptm160) cc_final: 0.7358 (ttm-80) REVERT: C 789 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9160 (tt) REVERT: C 1140 PHE cc_start: 0.8965 (m-80) cc_final: 0.8493 (m-80) REVERT: C 1181 PHE cc_start: 0.8582 (m-10) cc_final: 0.8328 (m-10) REVERT: C 1190 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8920 (mp0) REVERT: C 1191 MET cc_start: 0.9366 (mpp) cc_final: 0.8997 (mpp) REVERT: D 390 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3510 (mm) REVERT: D 503 MET cc_start: 0.8035 (tmm) cc_final: 0.7723 (tmm) REVERT: D 710 GLU cc_start: 0.8615 (pt0) cc_final: 0.8140 (tm-30) REVERT: D 721 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7792 (mpp) outliers start: 76 outliers final: 45 residues processed: 321 average time/residue: 0.3939 time to fit residues: 208.4912 Evaluate side-chains 297 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain C residue 1149 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 282 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 261 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 246 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31742 Z= 0.164 Angle : 0.546 10.515 42899 Z= 0.276 Chirality : 0.040 0.213 4762 Planarity : 0.004 0.057 5383 Dihedral : 5.319 57.412 4381 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 2.55 % Allowed : 12.49 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3897 helix: 1.80 (0.13), residues: 1752 sheet: -1.06 (0.26), residues: 412 loop : -2.33 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1032 HIS 0.004 0.001 HIS C1059 PHE 0.033 0.001 PHE A1181 TYR 0.018 0.001 TYR D1031 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 256 time to evaluate : 3.969 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: A 113 MET cc_start: 0.9159 (mmt) cc_final: 0.8599 (mmm) REVERT: A 369 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7488 (tpp80) REVERT: A 414 MET cc_start: 0.8783 (mpp) cc_final: 0.7959 (tpp) REVERT: A 728 ASP cc_start: 0.8107 (p0) cc_final: 0.7714 (m-30) REVERT: A 789 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 1009 MET cc_start: 0.8980 (tpp) cc_final: 0.8297 (mpp) REVERT: A 1126 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8854 (t80) REVERT: A 1140 PHE cc_start: 0.8974 (m-80) cc_final: 0.8535 (m-80) REVERT: A 1190 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9057 (mp0) REVERT: A 1199 MET cc_start: 0.9440 (tpp) cc_final: 0.9189 (tpp) REVERT: B 390 LEU cc_start: 0.4294 (OUTLIER) cc_final: 0.3594 (mm) REVERT: B 490 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (t0) REVERT: B 503 MET cc_start: 0.8188 (tmm) cc_final: 0.7569 (tmm) REVERT: B 710 GLU cc_start: 0.8584 (pt0) cc_final: 0.8158 (tm-30) REVERT: B 721 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7995 (mpp) REVERT: B 1069 GLU cc_start: 0.8669 (tp30) cc_final: 0.7986 (tt0) REVERT: B 1078 GLN cc_start: 0.7916 (tp40) cc_final: 0.7625 (tp40) REVERT: C 113 MET cc_start: 0.9165 (mmt) cc_final: 0.8602 (mmm) REVERT: C 369 ARG cc_start: 0.7743 (ptm160) cc_final: 0.7346 (ttm-80) REVERT: C 789 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9213 (tt) REVERT: C 1023 MET cc_start: 0.8428 (tpt) cc_final: 0.8182 (tpt) REVERT: C 1140 PHE cc_start: 0.8962 (m-80) cc_final: 0.8517 (m-80) REVERT: C 1181 PHE cc_start: 0.8553 (m-10) cc_final: 0.8336 (m-10) REVERT: C 1190 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8983 (mp0) REVERT: C 1191 MET cc_start: 0.9365 (mpp) cc_final: 0.8964 (mpp) REVERT: D 390 LEU cc_start: 0.4261 (OUTLIER) cc_final: 0.3535 (mm) REVERT: D 490 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8372 (t0) REVERT: D 503 MET cc_start: 0.8252 (tmm) cc_final: 0.7618 (tmm) REVERT: D 710 GLU cc_start: 0.8535 (pt0) cc_final: 0.8213 (tm-30) REVERT: D 1069 GLU cc_start: 0.8714 (tp30) cc_final: 0.8036 (tt0) outliers start: 85 outliers final: 54 residues processed: 313 average time/residue: 0.3873 time to fit residues: 200.8958 Evaluate side-chains 298 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 236 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain B residue 1207 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 20.0000 chunk 341 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 379 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31742 Z= 0.215 Angle : 0.572 9.939 42899 Z= 0.291 Chirality : 0.040 0.269 4762 Planarity : 0.004 0.056 5383 Dihedral : 5.085 47.512 4381 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.90 % Favored : 92.89 % Rotamer: Outliers : 2.70 % Allowed : 12.79 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.31 (0.14), residues: 3897 helix: 1.83 (0.13), residues: 1749 sheet: -1.07 (0.27), residues: 384 loop : -2.25 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1177 HIS 0.004 0.001 HIS A 46 PHE 0.050 0.001 PHE A1181 TYR 0.017 0.001 TYR D1031 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 240 time to evaluate : 3.671 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: A 113 MET cc_start: 0.9149 (mmt) cc_final: 0.8616 (mmm) REVERT: A 369 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7376 (tpp80) REVERT: A 728 ASP cc_start: 0.8152 (p0) cc_final: 0.7809 (m-30) REVERT: A 789 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9213 (tt) REVERT: A 1126 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8767 (t80) REVERT: A 1190 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9101 (mp0) REVERT: B 390 LEU cc_start: 0.4364 (OUTLIER) cc_final: 0.3707 (mm) REVERT: B 490 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (t0) REVERT: B 503 MET cc_start: 0.8324 (tmm) cc_final: 0.8020 (tmm) REVERT: B 527 MET cc_start: 0.8146 (tpt) cc_final: 0.7864 (tpt) REVERT: B 710 GLU cc_start: 0.8567 (pt0) cc_final: 0.8189 (tm-30) REVERT: B 721 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7956 (mpp) REVERT: B 1069 GLU cc_start: 0.8549 (tp30) cc_final: 0.8151 (tt0) REVERT: B 1078 GLN cc_start: 0.7984 (tp40) cc_final: 0.7760 (tp-100) REVERT: B 1191 MET cc_start: 0.9342 (tpp) cc_final: 0.8898 (tpt) REVERT: C 113 MET cc_start: 0.9153 (mmt) cc_final: 0.8622 (mmm) REVERT: C 369 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7336 (ttm-80) REVERT: C 789 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9260 (tt) REVERT: C 1181 PHE cc_start: 0.8604 (m-10) cc_final: 0.8330 (m-10) REVERT: C 1190 GLU cc_start: 0.9457 (mm-30) cc_final: 0.8980 (mp0) REVERT: C 1191 MET cc_start: 0.9359 (mpp) cc_final: 0.8988 (mpp) REVERT: D 390 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.3704 (mm) REVERT: D 490 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8416 (t0) REVERT: D 503 MET cc_start: 0.8195 (tmm) cc_final: 0.7927 (tmm) REVERT: D 527 MET cc_start: 0.8168 (tpt) cc_final: 0.7883 (tpt) REVERT: D 710 GLU cc_start: 0.8594 (pt0) cc_final: 0.8226 (tm-30) REVERT: D 1069 GLU cc_start: 0.8655 (tp30) cc_final: 0.8130 (tt0) REVERT: D 1191 MET cc_start: 0.9328 (tpp) cc_final: 0.8890 (tpt) outliers start: 90 outliers final: 68 residues processed: 303 average time/residue: 0.3933 time to fit residues: 196.3353 Evaluate side-chains 303 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 227 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1057 MET Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1066 CYS Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Chi-restraints excluded: chain D residue 1207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.0770 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 377 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 174 optimal weight: 0.0670 overall best weight: 3.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31742 Z= 0.282 Angle : 0.626 9.603 42899 Z= 0.319 Chirality : 0.041 0.274 4762 Planarity : 0.004 0.057 5383 Dihedral : 5.217 42.773 4381 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 2.79 % Allowed : 13.39 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.41 (0.14), residues: 3897 helix: 1.69 (0.13), residues: 1746 sheet: -1.07 (0.26), residues: 400 loop : -2.23 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1177 HIS 0.006 0.001 HIS A 46 PHE 0.045 0.002 PHE A1181 TYR 0.019 0.001 TYR C 711 ARG 0.005 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 223 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7301 (tpp80) REVERT: A 728 ASP cc_start: 0.8161 (p0) cc_final: 0.7947 (m-30) REVERT: A 1126 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8850 (t80) REVERT: A 1190 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9148 (mp0) REVERT: B 390 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4077 (mm) REVERT: B 503 MET cc_start: 0.8398 (tmm) cc_final: 0.8074 (tmm) REVERT: B 527 MET cc_start: 0.8165 (tpt) cc_final: 0.7898 (tpt) REVERT: B 710 GLU cc_start: 0.8627 (pt0) cc_final: 0.8231 (tm-30) REVERT: B 721 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8016 (mpp) REVERT: B 1069 GLU cc_start: 0.8607 (tp30) cc_final: 0.8244 (pt0) REVERT: C 369 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7389 (ttm-80) REVERT: C 1126 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8855 (t80) REVERT: C 1190 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9037 (mp0) REVERT: C 1191 MET cc_start: 0.9382 (mpp) cc_final: 0.9032 (mpp) REVERT: D 390 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.3927 (mm) REVERT: D 503 MET cc_start: 0.8291 (tmm) cc_final: 0.7990 (tmm) REVERT: D 527 MET cc_start: 0.8164 (tpt) cc_final: 0.7896 (tpt) REVERT: D 710 GLU cc_start: 0.8666 (pt0) cc_final: 0.8222 (tm-30) REVERT: D 1069 GLU cc_start: 0.8678 (tp30) cc_final: 0.7893 (tm-30) outliers start: 93 outliers final: 59 residues processed: 288 average time/residue: 0.3920 time to fit residues: 187.8747 Evaluate side-chains 277 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1057 MET Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 257 optimal weight: 0.4980 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 296 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 207 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31742 Z= 0.179 Angle : 0.585 12.749 42899 Z= 0.290 Chirality : 0.040 0.305 4762 Planarity : 0.003 0.052 5383 Dihedral : 4.963 40.135 4381 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.64 % Rotamer: Outliers : 2.16 % Allowed : 13.57 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.22 (0.14), residues: 3897 helix: 1.87 (0.13), residues: 1747 sheet: -1.01 (0.27), residues: 404 loop : -2.16 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 130 HIS 0.004 0.001 HIS A 46 PHE 0.045 0.001 PHE A1181 TYR 0.013 0.001 TYR D 673 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 230 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9120 (mmm) cc_final: 0.8547 (mmm) REVERT: A 369 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7339 (tpp80) REVERT: A 407 MET cc_start: 0.8970 (mmm) cc_final: 0.8754 (mmt) REVERT: A 1126 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8808 (t80) REVERT: A 1190 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9197 (mp0) REVERT: B 33 MET cc_start: 0.7901 (tpt) cc_final: 0.7588 (tpt) REVERT: B 390 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4331 (mm) REVERT: B 503 MET cc_start: 0.8273 (tmm) cc_final: 0.7908 (tmm) REVERT: B 527 MET cc_start: 0.8174 (tpt) cc_final: 0.7900 (tpt) REVERT: B 710 GLU cc_start: 0.8619 (pt0) cc_final: 0.8206 (tm-30) REVERT: B 721 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7985 (mpp) REVERT: B 1069 GLU cc_start: 0.8594 (tp30) cc_final: 0.8220 (pt0) REVERT: C 113 MET cc_start: 0.9122 (mmm) cc_final: 0.8546 (mmm) REVERT: C 369 ARG cc_start: 0.7690 (ptm160) cc_final: 0.7338 (ttm-80) REVERT: C 1126 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8848 (t80) REVERT: C 1181 PHE cc_start: 0.8541 (m-10) cc_final: 0.8293 (m-10) REVERT: C 1190 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9052 (mp0) REVERT: C 1191 MET cc_start: 0.9354 (mpp) cc_final: 0.9019 (mpp) REVERT: D 390 LEU cc_start: 0.4370 (OUTLIER) cc_final: 0.3777 (mm) REVERT: D 503 MET cc_start: 0.8213 (tmm) cc_final: 0.7903 (tmm) REVERT: D 527 MET cc_start: 0.8171 (tpt) cc_final: 0.7892 (tpt) REVERT: D 710 GLU cc_start: 0.8614 (pt0) cc_final: 0.8213 (tm-30) REVERT: D 1011 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8959 (mp) REVERT: D 1069 GLU cc_start: 0.8720 (tp30) cc_final: 0.7940 (tm-30) outliers start: 72 outliers final: 51 residues processed: 282 average time/residue: 0.3991 time to fit residues: 187.3561 Evaluate side-chains 276 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 767 TRP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1011 LEU Chi-restraints excluded: chain D residue 1013 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.2980 chunk 361 optimal weight: 0.9980 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 350 optimal weight: 0.0970 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS D 246 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31742 Z= 0.152 Angle : 0.576 11.797 42899 Z= 0.282 Chirality : 0.040 0.327 4762 Planarity : 0.003 0.050 5383 Dihedral : 4.728 36.731 4381 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.84 % Rotamer: Outliers : 1.62 % Allowed : 14.35 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.10 (0.14), residues: 3897 helix: 1.93 (0.13), residues: 1753 sheet: -0.93 (0.26), residues: 414 loop : -2.07 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 578 HIS 0.006 0.001 HIS C1059 PHE 0.037 0.001 PHE A1181 TYR 0.014 0.001 TYR C 405 ARG 0.004 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9077 (mmm) cc_final: 0.8619 (mmm) REVERT: A 369 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7321 (tpp80) REVERT: A 1126 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8798 (t80) REVERT: B 503 MET cc_start: 0.8236 (tmm) cc_final: 0.7839 (tmm) REVERT: B 527 MET cc_start: 0.8247 (tpt) cc_final: 0.7951 (tpt) REVERT: B 710 GLU cc_start: 0.8562 (pt0) cc_final: 0.8221 (tm-30) REVERT: B 721 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7940 (mpp) REVERT: B 1069 GLU cc_start: 0.8594 (tp30) cc_final: 0.8244 (pt0) REVERT: C 113 MET cc_start: 0.9072 (mmm) cc_final: 0.8612 (mmm) REVERT: C 369 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7411 (ttm-80) REVERT: C 1126 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8861 (t80) REVERT: C 1181 PHE cc_start: 0.8513 (m-10) cc_final: 0.8289 (m-10) REVERT: C 1190 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9073 (mp0) REVERT: C 1191 MET cc_start: 0.9336 (mpp) cc_final: 0.8988 (mpp) REVERT: D 225 LEU cc_start: 0.8462 (mt) cc_final: 0.8127 (mt) REVERT: D 390 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.3956 (mm) REVERT: D 503 MET cc_start: 0.8321 (tmm) cc_final: 0.7976 (tmm) REVERT: D 527 MET cc_start: 0.8260 (tpt) cc_final: 0.7967 (tpt) REVERT: D 710 GLU cc_start: 0.8593 (pt0) cc_final: 0.8245 (tm-30) REVERT: D 1069 GLU cc_start: 0.8735 (tp30) cc_final: 0.8261 (tt0) outliers start: 54 outliers final: 41 residues processed: 274 average time/residue: 0.3981 time to fit residues: 182.8595 Evaluate side-chains 269 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 1013 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1013 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.0770 chunk 372 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 258 optimal weight: 0.9990 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 147 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31742 Z= 0.149 Angle : 0.581 14.775 42899 Z= 0.282 Chirality : 0.040 0.299 4762 Planarity : 0.003 0.049 5383 Dihedral : 4.599 34.339 4381 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 1.59 % Allowed : 14.59 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.01 (0.14), residues: 3897 helix: 1.99 (0.13), residues: 1766 sheet: -0.80 (0.27), residues: 399 loop : -2.05 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 578 HIS 0.003 0.001 HIS C1059 PHE 0.035 0.001 PHE A1181 TYR 0.019 0.001 TYR D1031 ARG 0.004 0.000 ARG D 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7794 Ramachandran restraints generated. 3897 Oldfield, 0 Emsley, 3897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 233 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9056 (mmm) cc_final: 0.8622 (mmm) REVERT: A 1126 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8827 (t80) REVERT: B 503 MET cc_start: 0.8254 (tmm) cc_final: 0.7846 (tmm) REVERT: B 527 MET cc_start: 0.8235 (tpt) cc_final: 0.7943 (tpt) REVERT: B 721 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7916 (mpp) REVERT: B 1069 GLU cc_start: 0.8631 (tp30) cc_final: 0.8390 (tt0) REVERT: C 113 MET cc_start: 0.9053 (mmm) cc_final: 0.8630 (mmm) REVERT: C 369 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7401 (ttm-80) REVERT: C 1126 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8837 (t80) REVERT: C 1190 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9066 (mp0) REVERT: C 1191 MET cc_start: 0.9323 (mpp) cc_final: 0.8968 (mpp) REVERT: D 503 MET cc_start: 0.8328 (tmm) cc_final: 0.7980 (tmm) REVERT: D 527 MET cc_start: 0.8271 (tpt) cc_final: 0.7974 (tpt) REVERT: D 710 GLU cc_start: 0.8546 (pt0) cc_final: 0.8277 (tm-30) REVERT: D 1069 GLU cc_start: 0.8750 (tp30) cc_final: 0.8279 (tt0) outliers start: 53 outliers final: 43 residues processed: 266 average time/residue: 0.3784 time to fit residues: 169.3679 Evaluate side-chains 267 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1066 CYS Chi-restraints excluded: chain A residue 1126 PHE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1063 TRP Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1126 PHE Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain C residue 1147 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 1010 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 3.9990 chunk 331 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1198 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.077132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057675 restraints weight = 131258.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059360 restraints weight = 76914.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.060467 restraints weight = 55153.694| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31742 Z= 0.183 Angle : 0.593 14.389 42899 Z= 0.290 Chirality : 0.040 0.292 4762 Planarity : 0.004 0.074 5383 Dihedral : 4.612 33.154 4381 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Rotamer: Outliers : 1.62 % Allowed : 14.71 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.02 (0.14), residues: 3897 helix: 1.97 (0.13), residues: 1765 sheet: -0.92 (0.26), residues: 429 loop : -2.02 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 578 HIS 0.005 0.001 HIS C1059 PHE 0.037 0.001 PHE C1181 TYR 0.021 0.001 TYR D1031 ARG 0.004 0.000 ARG B 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5391.10 seconds wall clock time: 99 minutes 22.90 seconds (5962.90 seconds total)