Starting phenix.real_space_refine on Sat Feb 17 13:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnj_26011/02_2024/7tnj_26011_updated.pdb" } resolution = 4.02 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= 0.000 sd= 0.002 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 136 5.16 5 Cl 4 4.86 5 C 12212 2.51 5 N 3044 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.06, per 1000 atoms: 0.53 Number of scatterers: 18810 At special positions: 0 Unit cell: (128.65, 113.71, 135.29, 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 136 16.00 O 3414 8.00 N 3044 7.00 C 12212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.02 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 3.6 seconds 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 24 sheets defined 51.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.979A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.538A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.983A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 627 removed outlier: 3.636A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.707A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.597A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 781 through 784 removed outlier: 4.060A pdb=" N THR A 784 " --> pdb=" O LYS A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 784' 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: 3.753A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1027 removed outlier: 3.767A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 Processing helix chain 'A' and resid 1106 through 1124 removed outlier: 3.905A pdb=" N SER A1124 " --> pdb=" O CYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1160 removed outlier: 3.820A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A1158 " --> pdb=" O VAL A1154 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1207 removed outlier: 3.514A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 488 removed outlier: 4.101A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 623 removed outlier: 3.512A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) 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: 3.654A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.806A 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 694 removed outlier: 3.608A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.562A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.558A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 778 No H-bonds generated for 'chain 'B' and resid 775 through 778' Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 793 through 819 Processing helix chain 'B' and resid 1005 through 1028 removed outlier: 3.561A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B1028 " --> pdb=" O THR B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1093 through 1102 removed outlier: 3.546A pdb=" N LEU B1097 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1125 removed outlier: 3.518A pdb=" N CYS B1120 " --> pdb=" O MET B1116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B1121 " --> pdb=" O GLY B1117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B1122 " --> pdb=" O GLY B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1159 removed outlier: 3.688A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.512A pdb=" N ILE B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B1204 " --> pdb=" O PHE B1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.979A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.537A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.983A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 627 removed outlier: 3.636A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.706A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 712 Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.597A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 781 through 784 removed outlier: 4.059A pdb=" N THR C 784 " --> pdb=" O LYS C 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 781 through 784' 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: 3.753A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1027 removed outlier: 3.767A pdb=" N ALA C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1094 through 1102 Processing helix chain 'C' and resid 1106 through 1124 removed outlier: 3.904A pdb=" N SER C1124 " --> pdb=" O CYS C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1160 removed outlier: 3.821A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C1143 " --> pdb=" O ILE C1139 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C1158 " --> pdb=" O VAL C1154 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C1160 " --> pdb=" O ILE C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1207 removed outlier: 3.515A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.101A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 623 removed outlier: 3.512A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) 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 660 removed outlier: 3.653A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.806A 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 694 removed outlier: 3.609A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.561A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 769 removed outlier: 3.558A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 778 No H-bonds generated for 'chain 'D' and resid 775 through 778' Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 819 Processing helix chain 'D' and resid 1005 through 1028 removed outlier: 3.561A pdb=" N ALA D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D1028 " --> pdb=" O THR D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1102 removed outlier: 3.546A pdb=" N LEU D1097 " --> pdb=" O ALA D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1125 removed outlier: 3.518A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE D1121 " --> pdb=" O GLY D1117 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1159 removed outlier: 3.688A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 removed outlier: 3.512A pdb=" N ILE D1188 " --> pdb=" O LEU D1184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.697A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 454 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 459 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= D, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.750A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.632A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.806A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1064 through 1066 Processing sheet with id= H, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= I, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.626A pdb=" N ILE B 459 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.001A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1033 through 1036 Processing sheet with id= L, first strand: chain 'B' and resid 494 through 498 removed outlier: 7.120A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.697A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 454 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.750A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.633A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.807A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 1064 through 1066 Processing sheet with id= T, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= U, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.627A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.002A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1033 through 1036 Processing sheet with id= X, first strand: chain 'D' and resid 494 through 498 removed outlier: 7.120A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2610 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: 6.01 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5722 1.34 - 1.46: 4829 1.46 - 1.58: 8455 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19234 Sorted by residual: bond pdb=" N3 CYZ C1301 " pdb=" S2 CYZ C1301 " ideal model delta sigma weight residual 1.644 1.601 0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" N3 CYZ B1301 " pdb=" S2 CYZ B1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ A1301 " pdb=" S2 CYZ A1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" N3 CYZ D1301 " pdb=" S2 CYZ D1301 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.25e-02 6.40e+03 3.53e+00 ... (remaining 19229 not shown) Histogram of bond angle deviations from ideal: 93.30 - 101.53: 94 101.53 - 109.75: 2246 109.75 - 117.97: 12168 117.97 - 126.19: 11192 126.19 - 134.41: 286 Bond angle restraints: 25986 Sorted by residual: angle pdb=" N ASN D1132 " pdb=" CA ASN D1132 " pdb=" C ASN D1132 " ideal model delta sigma weight residual 114.56 107.79 6.77 1.27e+00 6.20e-01 2.84e+01 angle pdb=" C ASP A1091 " pdb=" N THR A1092 " pdb=" CA THR A1092 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" C LYS C1128 " pdb=" N THR C1129 " pdb=" CA THR C1129 " ideal model delta sigma weight residual 122.74 130.36 -7.62 1.44e+00 4.82e-01 2.80e+01 angle pdb=" C LYS A1128 " pdb=" N THR A1129 " pdb=" CA THR A1129 " ideal model delta sigma weight residual 122.74 130.35 -7.61 1.44e+00 4.82e-01 2.79e+01 ... (remaining 25981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 11038 24.42 - 48.84: 290 48.84 - 73.27: 18 73.27 - 97.69: 11 97.69 - 122.11: 9 Dihedral angle restraints: 11366 sinusoidal: 4488 harmonic: 6878 Sorted by residual: dihedral pdb=" CB CYS B1039 " pdb=" SG CYS B1039 " pdb=" SG CYS B1067 " pdb=" CB CYS B1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.68 52.32 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS D1039 " pdb=" SG CYS D1039 " pdb=" SG CYS D1067 " pdb=" CB CYS D1067 " ideal model delta sinusoidal sigma weight residual 93.00 40.74 52.26 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PRO D 632 " pdb=" C PRO D 632 " pdb=" N ILE D 633 " pdb=" CA ILE D 633 " ideal model delta harmonic sigma weight residual 180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2367 0.061 - 0.121: 439 0.121 - 0.182: 83 0.182 - 0.243: 13 0.243 - 0.304: 6 Chirality restraints: 2908 Sorted by residual: chirality pdb=" CB ILE D 525 " pdb=" CA ILE D 525 " pdb=" CG1 ILE D 525 " pdb=" CG2 ILE D 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE B 525 " pdb=" CA ILE B 525 " pdb=" CG1 ILE B 525 " pdb=" CG2 ILE B 525 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C8 CYZ A1301 " pdb=" C1 CYZ A1301 " pdb=" N1 CYZ A1301 " pdb=" N2 CYZ A1301 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2905 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D1088 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C TYR D1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR D1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU D1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B1088 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR B1088 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR B1088 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B1089 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 477 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 478 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.037 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4430 2.78 - 3.31: 17412 3.31 - 3.84: 30464 3.84 - 4.37: 36242 4.37 - 4.90: 60917 Nonbonded interactions: 149465 Sorted by model distance: nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASP C 760 " pdb="CL CYZ C1301 " model vdw 2.286 3.270 nonbonded pdb=" O THR D 643 " pdb=" OH TYR D 673 " model vdw 2.291 2.440 nonbonded pdb=" O THR B 643 " pdb=" OH TYR B 673 " model vdw 2.292 2.440 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.299 2.440 ... (remaining 149460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 394 through 549 or resid 565 through 1208 or resid 1301)) selection = chain 'C' selection = (chain 'D' and (resid 394 through 549 or resid 565 through 1208 or resid 1301)) } 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: 1.860 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: 0.020 Extract box with map and model: 7.660 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.540 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.005 0.070 19234 Z= 0.342 Angle : 0.941 10.572 25986 Z= 0.526 Chirality : 0.052 0.304 2908 Planarity : 0.007 0.067 3184 Dihedral : 11.627 122.110 6946 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.12), residues: 2362 helix: -3.76 (0.07), residues: 1314 sheet: -1.78 (0.36), residues: 170 loop : -2.34 (0.17), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C1032 HIS 0.005 0.001 HIS A1059 PHE 0.041 0.003 PHE C1082 TYR 0.042 0.002 TYR C1031 ARG 0.015 0.001 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 697 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 VAL cc_start: 0.8376 (t) cc_final: 0.7577 (t) REVERT: A 440 TYR cc_start: 0.7341 (p90) cc_final: 0.6726 (p90) REVERT: A 460 TRP cc_start: 0.4917 (m100) cc_final: 0.3952 (m100) REVERT: A 464 VAL cc_start: 0.8497 (t) cc_final: 0.8136 (p) REVERT: A 474 ILE cc_start: 0.8437 (tt) cc_final: 0.8210 (mp) REVERT: A 531 PHE cc_start: 0.8115 (m-10) cc_final: 0.7882 (m-80) REVERT: A 575 ASN cc_start: 0.8475 (m-40) cc_final: 0.8111 (m110) REVERT: A 671 TRP cc_start: 0.6522 (t-100) cc_final: 0.6078 (t60) REVERT: A 751 LEU cc_start: 0.9062 (mm) cc_final: 0.8855 (mp) REVERT: A 814 PHE cc_start: 0.6883 (t80) cc_final: 0.6469 (t80) REVERT: A 1128 LYS cc_start: 0.5014 (ttmm) cc_final: 0.4714 (tptt) REVERT: A 1171 ASN cc_start: 0.5165 (t160) cc_final: 0.4778 (t0) REVERT: B 401 LEU cc_start: 0.7746 (tt) cc_final: 0.7534 (tp) REVERT: B 496 MET cc_start: 0.8217 (ttp) cc_final: 0.7749 (ttp) REVERT: B 671 TRP cc_start: 0.5925 (t-100) cc_final: 0.5697 (t-100) REVERT: B 772 GLU cc_start: 0.7306 (pt0) cc_final: 0.6445 (mm-30) REVERT: B 1075 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7115 (tm) REVERT: C 442 LEU cc_start: 0.8075 (mt) cc_final: 0.7871 (mp) REVERT: C 460 TRP cc_start: 0.4414 (m100) cc_final: 0.3810 (m100) REVERT: C 578 TRP cc_start: 0.8950 (t-100) cc_final: 0.8749 (t-100) REVERT: C 642 GLN cc_start: 0.6559 (pp30) cc_final: 0.6291 (pp30) REVERT: C 671 TRP cc_start: 0.6350 (t-100) cc_final: 0.5903 (t60) REVERT: C 697 LYS cc_start: 0.7156 (mttm) cc_final: 0.6459 (pttp) REVERT: C 788 SER cc_start: 0.8173 (p) cc_final: 0.7894 (p) REVERT: C 800 VAL cc_start: 0.8002 (t) cc_final: 0.7513 (p) REVERT: C 1022 LEU cc_start: 0.6751 (mt) cc_final: 0.6478 (mt) REVERT: C 1105 ILE cc_start: 0.7611 (pt) cc_final: 0.7321 (pt) REVERT: C 1112 ILE cc_start: 0.8661 (mt) cc_final: 0.8443 (mm) REVERT: C 1140 PHE cc_start: 0.7940 (m-80) cc_final: 0.7681 (m-10) REVERT: C 1149 ILE cc_start: 0.8227 (tt) cc_final: 0.8015 (tp) REVERT: C 1173 TYR cc_start: 0.6741 (p90) cc_final: 0.5953 (p90) REVERT: D 427 ASP cc_start: 0.7690 (m-30) cc_final: 0.7342 (t70) REVERT: D 435 HIS cc_start: 0.6822 (m-70) cc_final: 0.6617 (m170) REVERT: D 508 GLN cc_start: 0.6986 (pm20) cc_final: 0.6352 (tt0) REVERT: D 713 GLU cc_start: 0.7233 (tt0) cc_final: 0.6919 (tm-30) REVERT: D 762 LEU cc_start: 0.8866 (mt) cc_final: 0.8396 (mt) REVERT: D 1009 MET cc_start: 0.7326 (ttp) cc_final: 0.7095 (ptm) REVERT: D 1023 MET cc_start: 0.7349 (tpt) cc_final: 0.6698 (ttm) REVERT: D 1075 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6855 (tm) REVERT: D 1139 ILE cc_start: 0.8220 (pt) cc_final: 0.7840 (mt) REVERT: D 1179 PHE cc_start: 0.8286 (t80) cc_final: 0.7960 (t80) outliers start: 4 outliers final: 1 residues processed: 701 average time/residue: 0.3212 time to fit residues: 332.3364 Evaluate side-chains 398 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 395 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 412 HIS B 714 GLN B 756 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN B1198 HIS C 714 GLN D 412 HIS D1008 GLN D1159 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 19234 Z= 0.314 Angle : 0.686 19.909 25986 Z= 0.364 Chirality : 0.044 0.538 2908 Planarity : 0.006 0.056 3184 Dihedral : 9.474 106.952 2698 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.35 % Allowed : 3.99 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.15), residues: 2362 helix: -0.85 (0.12), residues: 1350 sheet: -1.91 (0.35), residues: 162 loop : -1.90 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 671 HIS 0.004 0.001 HIS D1081 PHE 0.035 0.002 PHE B1017 TYR 0.022 0.002 TYR A1031 ARG 0.007 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 494 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8332 (tt) cc_final: 0.8043 (pt) REVERT: A 490 ASP cc_start: 0.7033 (m-30) cc_final: 0.6572 (m-30) REVERT: A 1009 MET cc_start: 0.7890 (tmm) cc_final: 0.7402 (tmm) REVERT: A 1201 ILE cc_start: 0.8174 (mm) cc_final: 0.7677 (mt) REVERT: B 772 GLU cc_start: 0.7126 (pt0) cc_final: 0.6171 (mm-30) REVERT: C 460 TRP cc_start: 0.4614 (m100) cc_final: 0.3621 (m100) REVERT: C 467 LEU cc_start: 0.8197 (tp) cc_final: 0.7921 (tt) REVERT: C 581 LEU cc_start: 0.8451 (tt) cc_final: 0.8236 (tp) REVERT: C 642 GLN cc_start: 0.6457 (pp30) cc_final: 0.6229 (pp30) REVERT: C 697 LYS cc_start: 0.7072 (mttm) cc_final: 0.6291 (pttp) REVERT: C 1128 LYS cc_start: 0.5850 (ttmm) cc_final: 0.5186 (tptp) REVERT: C 1156 ILE cc_start: 0.9122 (mt) cc_final: 0.8855 (mt) REVERT: C 1191 MET cc_start: 0.5997 (tpt) cc_final: 0.5601 (tpt) REVERT: C 1194 VAL cc_start: 0.8028 (t) cc_final: 0.7794 (p) REVERT: D 431 GLU cc_start: 0.6799 (tp30) cc_final: 0.6525 (tp30) REVERT: D 435 HIS cc_start: 0.6292 (m-70) cc_final: 0.5825 (m-70) REVERT: D 508 GLN cc_start: 0.7071 (pm20) cc_final: 0.6332 (tt0) REVERT: D 645 ILE cc_start: 0.6793 (mm) cc_final: 0.6397 (tt) REVERT: D 656 LYS cc_start: 0.7087 (ptmt) cc_final: 0.6688 (ptmm) REVERT: D 713 GLU cc_start: 0.7419 (tt0) cc_final: 0.7127 (tm-30) REVERT: D 752 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7780 (ttpt) REVERT: D 772 GLU cc_start: 0.6752 (pt0) cc_final: 0.6161 (mm-30) REVERT: D 1017 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4446 (m-10) REVERT: D 1023 MET cc_start: 0.7449 (tpt) cc_final: 0.6454 (ttt) REVERT: D 1027 VAL cc_start: 0.8199 (t) cc_final: 0.7886 (m) REVERT: D 1031 TYR cc_start: 0.6147 (m-80) cc_final: 0.5908 (m-80) REVERT: D 1139 ILE cc_start: 0.8293 (pt) cc_final: 0.7916 (mt) REVERT: D 1179 PHE cc_start: 0.8063 (t80) cc_final: 0.7857 (t80) REVERT: D 1190 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7632 (mm-30) REVERT: D 1206 GLN cc_start: 0.3787 (mp10) cc_final: 0.2733 (tp40) outliers start: 7 outliers final: 0 residues processed: 498 average time/residue: 0.2804 time to fit residues: 216.3087 Evaluate side-chains 361 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN B1159 ASN C 642 GLN D1159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19234 Z= 0.198 Angle : 0.568 10.086 25986 Z= 0.300 Chirality : 0.041 0.331 2908 Planarity : 0.004 0.050 3184 Dihedral : 8.971 102.723 2698 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.20 % Allowed : 3.19 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2362 helix: 0.53 (0.14), residues: 1312 sheet: -1.86 (0.35), residues: 164 loop : -1.74 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 671 HIS 0.012 0.001 HIS A1204 PHE 0.029 0.002 PHE B1017 TYR 0.021 0.001 TYR A1031 ARG 0.005 0.001 ARG A1203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 456 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7140 (p90) cc_final: 0.6894 (p90) REVERT: A 460 TRP cc_start: 0.5035 (m100) cc_final: 0.3958 (m100) REVERT: A 490 ASP cc_start: 0.7041 (m-30) cc_final: 0.6642 (m-30) REVERT: A 697 LYS cc_start: 0.7504 (mttm) cc_final: 0.6403 (pttp) REVERT: A 1009 MET cc_start: 0.7861 (tmm) cc_final: 0.7374 (tmm) REVERT: B 772 GLU cc_start: 0.6992 (pt0) cc_final: 0.6522 (mm-30) REVERT: B 1173 TYR cc_start: 0.6210 (p90) cc_final: 0.3645 (m-80) REVERT: C 440 TYR cc_start: 0.7383 (p90) cc_final: 0.7089 (p90) REVERT: C 460 TRP cc_start: 0.4539 (m100) cc_final: 0.3577 (m100) REVERT: C 467 LEU cc_start: 0.8160 (tp) cc_final: 0.7901 (tt) REVERT: C 697 LYS cc_start: 0.7109 (mttm) cc_final: 0.6237 (pttp) REVERT: C 1098 ARG cc_start: 0.6885 (mtp180) cc_final: 0.6261 (ptm160) REVERT: C 1128 LYS cc_start: 0.5777 (ttmm) cc_final: 0.5115 (tptp) REVERT: C 1191 MET cc_start: 0.6134 (tpt) cc_final: 0.5749 (tpt) REVERT: D 435 HIS cc_start: 0.6274 (m-70) cc_final: 0.5845 (m170) REVERT: D 508 GLN cc_start: 0.6940 (pm20) cc_final: 0.6271 (tt0) REVERT: D 527 MET cc_start: 0.7952 (tmm) cc_final: 0.7428 (ttp) REVERT: D 709 ASN cc_start: 0.8790 (t0) cc_final: 0.8539 (t0) REVERT: D 713 GLU cc_start: 0.7352 (tt0) cc_final: 0.7100 (tm-30) REVERT: D 752 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7777 (ttpt) REVERT: D 772 GLU cc_start: 0.6502 (pt0) cc_final: 0.6076 (mm-30) REVERT: D 1009 MET cc_start: 0.6997 (ptm) cc_final: 0.6797 (ptm) REVERT: D 1023 MET cc_start: 0.7356 (tpt) cc_final: 0.6433 (ttm) REVERT: D 1027 VAL cc_start: 0.8203 (t) cc_final: 0.7916 (m) REVERT: D 1116 MET cc_start: 0.7033 (mtt) cc_final: 0.6783 (mpp) REVERT: D 1139 ILE cc_start: 0.8175 (pt) cc_final: 0.7824 (mt) REVERT: D 1179 PHE cc_start: 0.8068 (t80) cc_final: 0.7813 (t80) REVERT: D 1190 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7525 (mm-30) outliers start: 4 outliers final: 0 residues processed: 458 average time/residue: 0.2632 time to fit residues: 190.9911 Evaluate side-chains 345 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 0.0370 chunk 61 optimal weight: 10.0000 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 619 ASN D 587 GLN D1159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19234 Z= 0.210 Angle : 0.567 6.843 25986 Z= 0.298 Chirality : 0.040 0.196 2908 Planarity : 0.004 0.053 3184 Dihedral : 8.604 96.493 2698 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.15 % Allowed : 3.64 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2362 helix: 1.07 (0.14), residues: 1312 sheet: -1.77 (0.35), residues: 176 loop : -1.56 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1032 HIS 0.007 0.001 HIS B1198 PHE 0.022 0.002 PHE D 574 TYR 0.020 0.001 TYR A1031 ARG 0.004 0.001 ARG A1203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 444 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7193 (p90) cc_final: 0.6941 (p90) REVERT: A 460 TRP cc_start: 0.5013 (m100) cc_final: 0.3952 (m100) REVERT: A 490 ASP cc_start: 0.7154 (m-30) cc_final: 0.6717 (m-30) REVERT: A 697 LYS cc_start: 0.7543 (mttm) cc_final: 0.6425 (pttp) REVERT: A 713 GLU cc_start: 0.6963 (tt0) cc_final: 0.6193 (tt0) REVERT: A 772 GLU cc_start: 0.6654 (pm20) cc_final: 0.5561 (mm-30) REVERT: A 817 LYS cc_start: 0.5510 (mmmt) cc_final: 0.5275 (mmmt) REVERT: A 1009 MET cc_start: 0.7832 (tmm) cc_final: 0.7585 (tmm) REVERT: A 1032 TRP cc_start: 0.8197 (m-10) cc_final: 0.7908 (m-10) REVERT: A 1096 PHE cc_start: 0.7277 (m-10) cc_final: 0.6978 (m-10) REVERT: B 431 GLU cc_start: 0.6529 (tp30) cc_final: 0.6311 (tp30) REVERT: B 772 GLU cc_start: 0.7040 (pt0) cc_final: 0.6508 (mm-30) REVERT: B 1173 TYR cc_start: 0.6397 (p90) cc_final: 0.3744 (m-80) REVERT: B 1188 ILE cc_start: 0.7852 (mm) cc_final: 0.7629 (mm) REVERT: C 440 TYR cc_start: 0.7402 (p90) cc_final: 0.6888 (p90) REVERT: C 460 TRP cc_start: 0.4710 (m100) cc_final: 0.3684 (m100) REVERT: C 467 LEU cc_start: 0.8221 (tp) cc_final: 0.8008 (tt) REVERT: C 600 ILE cc_start: 0.8400 (mt) cc_final: 0.8158 (mp) REVERT: C 697 LYS cc_start: 0.7138 (mttm) cc_final: 0.6309 (pttp) REVERT: C 772 GLU cc_start: 0.6782 (pm20) cc_final: 0.5594 (mm-30) REVERT: C 1128 LYS cc_start: 0.5802 (ttmm) cc_final: 0.5131 (tptp) REVERT: C 1191 MET cc_start: 0.6054 (tpt) cc_final: 0.5744 (tpt) REVERT: D 508 GLN cc_start: 0.6977 (pm20) cc_final: 0.6226 (tt0) REVERT: D 527 MET cc_start: 0.7924 (tmm) cc_final: 0.7450 (ttp) REVERT: D 709 ASN cc_start: 0.8742 (t0) cc_final: 0.8484 (t0) REVERT: D 713 GLU cc_start: 0.7441 (tt0) cc_final: 0.7120 (tm-30) REVERT: D 772 GLU cc_start: 0.6434 (pt0) cc_final: 0.6012 (mm-30) REVERT: D 1009 MET cc_start: 0.7049 (ptm) cc_final: 0.6833 (ptm) REVERT: D 1023 MET cc_start: 0.7268 (tpt) cc_final: 0.6363 (ttm) REVERT: D 1027 VAL cc_start: 0.8245 (t) cc_final: 0.7940 (m) REVERT: D 1116 MET cc_start: 0.7029 (mtt) cc_final: 0.6750 (mtt) REVERT: D 1139 ILE cc_start: 0.8202 (pt) cc_final: 0.7783 (mt) REVERT: D 1179 PHE cc_start: 0.8017 (t80) cc_final: 0.7734 (t80) REVERT: D 1188 ILE cc_start: 0.8156 (mm) cc_final: 0.7926 (mm) outliers start: 3 outliers final: 0 residues processed: 446 average time/residue: 0.2642 time to fit residues: 186.6801 Evaluate side-chains 347 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 171 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 206 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19234 Z= 0.155 Angle : 0.529 6.048 25986 Z= 0.275 Chirality : 0.039 0.176 2908 Planarity : 0.004 0.052 3184 Dihedral : 7.985 90.974 2698 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2362 helix: 1.43 (0.14), residues: 1324 sheet: -1.69 (0.35), residues: 188 loop : -1.45 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1032 HIS 0.004 0.001 HIS B1198 PHE 0.021 0.001 PHE B1141 TYR 0.017 0.001 TYR A1031 ARG 0.006 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: A 460 TRP cc_start: 0.4911 (m100) cc_final: 0.3925 (m100) REVERT: A 490 ASP cc_start: 0.7089 (m-30) cc_final: 0.6766 (t70) REVERT: A 697 LYS cc_start: 0.7486 (mttm) cc_final: 0.6455 (pttp) REVERT: A 772 GLU cc_start: 0.6483 (pm20) cc_final: 0.5540 (mm-30) REVERT: A 1004 ASP cc_start: 0.6108 (t0) cc_final: 0.5749 (m-30) REVERT: A 1009 MET cc_start: 0.7820 (tmm) cc_final: 0.7557 (tmm) REVERT: A 1032 TRP cc_start: 0.8091 (m-10) cc_final: 0.7845 (m-10) REVERT: B 431 GLU cc_start: 0.6665 (tp30) cc_final: 0.6388 (tp30) REVERT: B 772 GLU cc_start: 0.6969 (pt0) cc_final: 0.6398 (mm-30) REVERT: B 1173 TYR cc_start: 0.6511 (p90) cc_final: 0.3878 (m-80) REVERT: B 1188 ILE cc_start: 0.7800 (mm) cc_final: 0.7585 (mm) REVERT: C 440 TYR cc_start: 0.7408 (p90) cc_final: 0.6917 (p90) REVERT: C 460 TRP cc_start: 0.4640 (m100) cc_final: 0.3652 (m100) REVERT: C 467 LEU cc_start: 0.8171 (tp) cc_final: 0.7966 (tt) REVERT: C 697 LYS cc_start: 0.7131 (mttm) cc_final: 0.6239 (pttp) REVERT: C 772 GLU cc_start: 0.6797 (pm20) cc_final: 0.5609 (mm-30) REVERT: C 1057 MET cc_start: 0.6150 (ttt) cc_final: 0.5675 (ttm) REVERT: C 1098 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6006 (mmt90) REVERT: C 1105 ILE cc_start: 0.8121 (pt) cc_final: 0.7774 (tp) REVERT: C 1128 LYS cc_start: 0.5766 (ttmm) cc_final: 0.5092 (tptp) REVERT: D 500 ILE cc_start: 0.8566 (mm) cc_final: 0.8257 (mm) REVERT: D 508 GLN cc_start: 0.6938 (pm20) cc_final: 0.6160 (tt0) REVERT: D 527 MET cc_start: 0.7878 (tmm) cc_final: 0.7466 (ttp) REVERT: D 709 ASN cc_start: 0.8677 (t0) cc_final: 0.8406 (t0) REVERT: D 713 GLU cc_start: 0.7352 (tt0) cc_final: 0.7101 (tm-30) REVERT: D 772 GLU cc_start: 0.6451 (pt0) cc_final: 0.5958 (mm-30) REVERT: D 1009 MET cc_start: 0.6999 (ptm) cc_final: 0.6761 (ptm) REVERT: D 1023 MET cc_start: 0.7218 (tpt) cc_final: 0.6390 (mtp) REVERT: D 1027 VAL cc_start: 0.8280 (t) cc_final: 0.7977 (m) REVERT: D 1175 TYR cc_start: 0.5692 (m-80) cc_final: 0.4832 (m-10) REVERT: D 1179 PHE cc_start: 0.8016 (t80) cc_final: 0.7544 (t80) REVERT: D 1188 ILE cc_start: 0.8032 (mm) cc_final: 0.7823 (mm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2782 time to fit residues: 198.7283 Evaluate side-chains 353 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 230 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN ** D1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19234 Z= 0.157 Angle : 0.526 6.878 25986 Z= 0.273 Chirality : 0.039 0.194 2908 Planarity : 0.003 0.048 3184 Dihedral : 7.389 86.941 2698 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2362 helix: 1.63 (0.14), residues: 1316 sheet: -1.61 (0.36), residues: 178 loop : -1.37 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C1032 HIS 0.003 0.001 HIS B1198 PHE 0.020 0.001 PHE B1141 TYR 0.016 0.001 TYR C1031 ARG 0.005 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7025 (p90) cc_final: 0.6667 (p90) REVERT: A 460 TRP cc_start: 0.4925 (m100) cc_final: 0.3766 (m100) REVERT: A 490 ASP cc_start: 0.7083 (m-30) cc_final: 0.6728 (t70) REVERT: A 697 LYS cc_start: 0.7421 (mttm) cc_final: 0.6426 (pttp) REVERT: A 772 GLU cc_start: 0.6508 (pm20) cc_final: 0.5626 (mm-30) REVERT: A 1009 MET cc_start: 0.7742 (tmm) cc_final: 0.7493 (tmm) REVERT: A 1032 TRP cc_start: 0.8030 (m-10) cc_final: 0.7751 (m-10) REVERT: A 1077 LYS cc_start: 0.6371 (ptmt) cc_final: 0.6056 (ptpt) REVERT: A 1096 PHE cc_start: 0.7208 (m-10) cc_final: 0.6981 (m-10) REVERT: B 431 GLU cc_start: 0.6734 (tp30) cc_final: 0.6478 (tp30) REVERT: B 772 GLU cc_start: 0.6764 (pt0) cc_final: 0.6296 (mm-30) REVERT: B 1173 TYR cc_start: 0.6576 (p90) cc_final: 0.3953 (m-80) REVERT: B 1179 PHE cc_start: 0.8380 (t80) cc_final: 0.8175 (t80) REVERT: B 1188 ILE cc_start: 0.7784 (mm) cc_final: 0.7531 (mm) REVERT: C 440 TYR cc_start: 0.7385 (p90) cc_final: 0.6876 (p90) REVERT: C 460 TRP cc_start: 0.4590 (m100) cc_final: 0.3527 (m100) REVERT: C 467 LEU cc_start: 0.8141 (tp) cc_final: 0.7932 (tt) REVERT: C 697 LYS cc_start: 0.7192 (mttm) cc_final: 0.6311 (pttp) REVERT: C 772 GLU cc_start: 0.6718 (pm20) cc_final: 0.5713 (mm-30) REVERT: C 1057 MET cc_start: 0.6168 (ttt) cc_final: 0.5700 (ttm) REVERT: C 1098 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6039 (mmt90) REVERT: C 1105 ILE cc_start: 0.8131 (pt) cc_final: 0.7835 (tp) REVERT: C 1128 LYS cc_start: 0.5725 (ttmm) cc_final: 0.5069 (tptp) REVERT: D 464 VAL cc_start: 0.8204 (t) cc_final: 0.7981 (t) REVERT: D 500 ILE cc_start: 0.8548 (mm) cc_final: 0.8243 (mm) REVERT: D 508 GLN cc_start: 0.6955 (pm20) cc_final: 0.6172 (tt0) REVERT: D 527 MET cc_start: 0.7896 (tmm) cc_final: 0.7561 (ttp) REVERT: D 709 ASN cc_start: 0.8650 (t0) cc_final: 0.8448 (t0) REVERT: D 713 GLU cc_start: 0.7380 (tt0) cc_final: 0.7081 (tm-30) REVERT: D 772 GLU cc_start: 0.6373 (pt0) cc_final: 0.5940 (mm-30) REVERT: D 1009 MET cc_start: 0.7058 (ptm) cc_final: 0.6747 (ptm) REVERT: D 1023 MET cc_start: 0.7225 (tpt) cc_final: 0.6289 (mtp) REVERT: D 1027 VAL cc_start: 0.8321 (t) cc_final: 0.8000 (m) REVERT: D 1175 TYR cc_start: 0.5703 (m-80) cc_final: 0.4816 (m-10) REVERT: D 1179 PHE cc_start: 0.8032 (t80) cc_final: 0.7590 (t80) REVERT: D 1191 MET cc_start: 0.6958 (mtp) cc_final: 0.5533 (tpp) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.2640 time to fit residues: 185.0646 Evaluate side-chains 353 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 0.2980 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 619 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19234 Z= 0.190 Angle : 0.552 6.581 25986 Z= 0.288 Chirality : 0.040 0.209 2908 Planarity : 0.004 0.049 3184 Dihedral : 7.045 87.417 2698 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2362 helix: 1.67 (0.14), residues: 1310 sheet: -1.55 (0.38), residues: 164 loop : -1.31 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1177 HIS 0.003 0.001 HIS B1198 PHE 0.021 0.001 PHE B1017 TYR 0.017 0.001 TYR C1031 ARG 0.004 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 421 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7068 (p90) cc_final: 0.6688 (p90) REVERT: A 460 TRP cc_start: 0.4928 (m100) cc_final: 0.3882 (m100) REVERT: A 490 ASP cc_start: 0.7087 (m-30) cc_final: 0.6740 (t70) REVERT: A 697 LYS cc_start: 0.7295 (mttm) cc_final: 0.6388 (pttp) REVERT: A 713 GLU cc_start: 0.7169 (tt0) cc_final: 0.6872 (tt0) REVERT: A 772 GLU cc_start: 0.6246 (pm20) cc_final: 0.5426 (mm-30) REVERT: A 814 PHE cc_start: 0.7078 (t80) cc_final: 0.6740 (t80) REVERT: A 816 TYR cc_start: 0.5738 (t80) cc_final: 0.5534 (t80) REVERT: A 1009 MET cc_start: 0.7783 (tmm) cc_final: 0.7541 (tmm) REVERT: A 1032 TRP cc_start: 0.7998 (m-10) cc_final: 0.7764 (m-10) REVERT: B 431 GLU cc_start: 0.7000 (tp30) cc_final: 0.6780 (tp30) REVERT: B 772 GLU cc_start: 0.6579 (pt0) cc_final: 0.6128 (mm-30) REVERT: B 1173 TYR cc_start: 0.6658 (p90) cc_final: 0.3994 (m-80) REVERT: B 1179 PHE cc_start: 0.8396 (t80) cc_final: 0.8195 (t80) REVERT: C 440 TYR cc_start: 0.7313 (p90) cc_final: 0.6799 (p90) REVERT: C 460 TRP cc_start: 0.4500 (m100) cc_final: 0.3439 (m100) REVERT: C 467 LEU cc_start: 0.8187 (tp) cc_final: 0.7978 (tt) REVERT: C 697 LYS cc_start: 0.7212 (mttm) cc_final: 0.6375 (pttp) REVERT: C 772 GLU cc_start: 0.6488 (pm20) cc_final: 0.5431 (mm-30) REVERT: C 1057 MET cc_start: 0.6216 (ttt) cc_final: 0.5748 (ttm) REVERT: C 1098 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6130 (mmt90) REVERT: C 1105 ILE cc_start: 0.8157 (pt) cc_final: 0.7817 (tp) REVERT: C 1128 LYS cc_start: 0.5687 (ttmm) cc_final: 0.5020 (tptp) REVERT: C 1149 ILE cc_start: 0.8765 (tt) cc_final: 0.8530 (tp) REVERT: D 500 ILE cc_start: 0.8569 (mm) cc_final: 0.8278 (mm) REVERT: D 508 GLN cc_start: 0.7014 (pm20) cc_final: 0.6166 (tt0) REVERT: D 527 MET cc_start: 0.7876 (tmm) cc_final: 0.7594 (ttp) REVERT: D 709 ASN cc_start: 0.8672 (t0) cc_final: 0.8443 (t0) REVERT: D 713 GLU cc_start: 0.7420 (tt0) cc_final: 0.6919 (tm-30) REVERT: D 772 GLU cc_start: 0.6280 (pt0) cc_final: 0.5903 (mm-30) REVERT: D 1009 MET cc_start: 0.7122 (ptm) cc_final: 0.6815 (ptm) REVERT: D 1023 MET cc_start: 0.7159 (tpt) cc_final: 0.6140 (ttm) REVERT: D 1027 VAL cc_start: 0.8350 (t) cc_final: 0.7995 (m) REVERT: D 1179 PHE cc_start: 0.8028 (t80) cc_final: 0.7669 (t80) REVERT: D 1188 ILE cc_start: 0.7983 (mm) cc_final: 0.7730 (mm) REVERT: D 1191 MET cc_start: 0.6968 (mtp) cc_final: 0.5575 (tpp) outliers start: 2 outliers final: 0 residues processed: 422 average time/residue: 0.2644 time to fit residues: 178.2834 Evaluate side-chains 338 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.0000 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 180 optimal weight: 0.0570 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19234 Z= 0.148 Angle : 0.529 7.697 25986 Z= 0.274 Chirality : 0.040 0.206 2908 Planarity : 0.003 0.042 3184 Dihedral : 6.574 82.683 2698 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2362 helix: 1.83 (0.14), residues: 1310 sheet: -1.61 (0.36), residues: 176 loop : -1.36 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1177 HIS 0.013 0.001 HIS A 435 PHE 0.026 0.001 PHE A1115 TYR 0.030 0.001 TYR D 647 ARG 0.007 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7043 (p90) cc_final: 0.6680 (p90) REVERT: A 460 TRP cc_start: 0.4804 (m100) cc_final: 0.3764 (m100) REVERT: A 490 ASP cc_start: 0.7051 (m-30) cc_final: 0.6719 (t70) REVERT: A 528 CYS cc_start: 0.8255 (m) cc_final: 0.7943 (m) REVERT: A 697 LYS cc_start: 0.7260 (mttm) cc_final: 0.6399 (pttp) REVERT: A 713 GLU cc_start: 0.7133 (tt0) cc_final: 0.6832 (tt0) REVERT: A 772 GLU cc_start: 0.6225 (pm20) cc_final: 0.5445 (mm-30) REVERT: A 814 PHE cc_start: 0.6988 (t80) cc_final: 0.6657 (t80) REVERT: A 816 TYR cc_start: 0.5764 (t80) cc_final: 0.5550 (t80) REVERT: A 1009 MET cc_start: 0.7760 (tmm) cc_final: 0.7529 (tmm) REVERT: B 431 GLU cc_start: 0.7065 (tp30) cc_final: 0.6835 (tp30) REVERT: B 709 ASN cc_start: 0.8614 (t0) cc_final: 0.8411 (t0) REVERT: B 772 GLU cc_start: 0.6586 (pt0) cc_final: 0.6163 (mm-30) REVERT: B 1173 TYR cc_start: 0.6642 (p90) cc_final: 0.3988 (m-80) REVERT: C 440 TYR cc_start: 0.7312 (p90) cc_final: 0.6777 (p90) REVERT: C 460 TRP cc_start: 0.4506 (m100) cc_final: 0.3451 (m100) REVERT: C 467 LEU cc_start: 0.8113 (tp) cc_final: 0.7903 (tt) REVERT: C 657 GLU cc_start: 0.7745 (pt0) cc_final: 0.7075 (tp30) REVERT: C 697 LYS cc_start: 0.7195 (mttm) cc_final: 0.6493 (pttp) REVERT: C 772 GLU cc_start: 0.6334 (pm20) cc_final: 0.5401 (mm-30) REVERT: C 1032 TRP cc_start: 0.7830 (m-10) cc_final: 0.7447 (m-10) REVERT: C 1057 MET cc_start: 0.6198 (ttt) cc_final: 0.5739 (ttm) REVERT: C 1098 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6081 (mmt90) REVERT: C 1105 ILE cc_start: 0.8161 (pt) cc_final: 0.7854 (tp) REVERT: C 1128 LYS cc_start: 0.5587 (ttmm) cc_final: 0.4971 (tptp) REVERT: D 500 ILE cc_start: 0.8557 (mm) cc_final: 0.8281 (mm) REVERT: D 508 GLN cc_start: 0.7030 (pm20) cc_final: 0.6177 (tt0) REVERT: D 527 MET cc_start: 0.7841 (tmm) cc_final: 0.7559 (ttp) REVERT: D 713 GLU cc_start: 0.7395 (tt0) cc_final: 0.6858 (tm-30) REVERT: D 772 GLU cc_start: 0.6202 (pt0) cc_final: 0.5852 (mm-30) REVERT: D 1009 MET cc_start: 0.7008 (ptm) cc_final: 0.6698 (ptm) REVERT: D 1023 MET cc_start: 0.7135 (tpt) cc_final: 0.6175 (mtp) REVERT: D 1027 VAL cc_start: 0.8351 (t) cc_final: 0.8010 (m) REVERT: D 1063 TRP cc_start: 0.4711 (m100) cc_final: 0.4348 (m100) REVERT: D 1179 PHE cc_start: 0.7979 (t80) cc_final: 0.7658 (t80) REVERT: D 1188 ILE cc_start: 0.7969 (mm) cc_final: 0.7721 (mm) REVERT: D 1191 MET cc_start: 0.6920 (mtp) cc_final: 0.5505 (tpp) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.2649 time to fit residues: 182.8507 Evaluate side-chains 354 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN B1159 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 19234 Z= 0.387 Angle : 0.721 9.660 25986 Z= 0.378 Chirality : 0.046 0.220 2908 Planarity : 0.005 0.075 3184 Dihedral : 7.400 93.478 2698 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.20 % Allowed : 1.05 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.06 (0.17), residues: 2362 helix: 1.14 (0.14), residues: 1304 sheet: -1.73 (0.36), residues: 172 loop : -1.46 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1032 HIS 0.007 0.002 HIS C1131 PHE 0.030 0.002 PHE C1082 TYR 0.029 0.002 TYR C1031 ARG 0.011 0.001 ARG D 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 389 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7101 (p90) cc_final: 0.6654 (p90) REVERT: A 460 TRP cc_start: 0.5202 (m100) cc_final: 0.4044 (m100) REVERT: A 697 LYS cc_start: 0.7230 (mttm) cc_final: 0.6386 (pttp) REVERT: A 713 GLU cc_start: 0.7234 (tt0) cc_final: 0.6906 (tt0) REVERT: A 772 GLU cc_start: 0.6290 (pm20) cc_final: 0.5730 (mm-30) REVERT: A 814 PHE cc_start: 0.7144 (t80) cc_final: 0.6800 (t80) REVERT: B 487 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7370 (tt0) REVERT: B 772 GLU cc_start: 0.6538 (pt0) cc_final: 0.6229 (mm-30) REVERT: B 1023 MET cc_start: 0.7007 (mmm) cc_final: 0.6083 (mtt) REVERT: B 1175 TYR cc_start: 0.5080 (m-80) cc_final: 0.4800 (m-10) REVERT: B 1191 MET cc_start: 0.6016 (tpp) cc_final: 0.5608 (tpp) REVERT: C 440 TYR cc_start: 0.7333 (p90) cc_final: 0.6835 (p90) REVERT: C 467 LEU cc_start: 0.8217 (tp) cc_final: 0.7969 (tt) REVERT: C 657 GLU cc_start: 0.7839 (pt0) cc_final: 0.7278 (tp30) REVERT: C 697 LYS cc_start: 0.7210 (mttm) cc_final: 0.6455 (pttp) REVERT: C 772 GLU cc_start: 0.6584 (pm20) cc_final: 0.5732 (mm-30) REVERT: C 1003 PHE cc_start: 0.4449 (p90) cc_final: 0.4002 (m-80) REVERT: C 1032 TRP cc_start: 0.8097 (m-10) cc_final: 0.7524 (m-10) REVERT: C 1057 MET cc_start: 0.6316 (ttt) cc_final: 0.5888 (ttm) REVERT: C 1128 LYS cc_start: 0.5667 (ttmm) cc_final: 0.5008 (tptp) REVERT: D 508 GLN cc_start: 0.6946 (pm20) cc_final: 0.6156 (tt0) REVERT: D 713 GLU cc_start: 0.7524 (tt0) cc_final: 0.7093 (tm-30) REVERT: D 772 GLU cc_start: 0.6282 (pt0) cc_final: 0.6011 (mm-30) REVERT: D 1009 MET cc_start: 0.7068 (ptm) cc_final: 0.6770 (ptm) REVERT: D 1023 MET cc_start: 0.7097 (tpt) cc_final: 0.6128 (ttm) REVERT: D 1027 VAL cc_start: 0.8366 (t) cc_final: 0.8035 (m) REVERT: D 1060 SER cc_start: 0.7820 (m) cc_final: 0.7345 (p) REVERT: D 1179 PHE cc_start: 0.8117 (t80) cc_final: 0.7799 (t80) REVERT: D 1188 ILE cc_start: 0.8035 (mm) cc_final: 0.7834 (mm) outliers start: 4 outliers final: 1 residues processed: 392 average time/residue: 0.2613 time to fit residues: 163.2849 Evaluate side-chains 323 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B1159 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19234 Z= 0.174 Angle : 0.594 11.620 25986 Z= 0.309 Chirality : 0.041 0.252 2908 Planarity : 0.004 0.037 3184 Dihedral : 6.853 87.242 2698 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2362 helix: 1.49 (0.14), residues: 1310 sheet: -1.81 (0.36), residues: 176 loop : -1.37 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1032 HIS 0.006 0.001 HIS C 435 PHE 0.031 0.002 PHE C1082 TYR 0.025 0.001 TYR C1031 ARG 0.005 0.000 ARG C 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4724 Ramachandran restraints generated. 2362 Oldfield, 0 Emsley, 2362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 TYR cc_start: 0.7075 (p90) cc_final: 0.6602 (p90) REVERT: A 460 TRP cc_start: 0.5091 (m100) cc_final: 0.3979 (m100) REVERT: A 474 ILE cc_start: 0.8178 (tt) cc_final: 0.7941 (pt) REVERT: A 490 ASP cc_start: 0.7364 (m-30) cc_final: 0.6981 (m-30) REVERT: A 528 CYS cc_start: 0.8251 (m) cc_final: 0.7954 (m) REVERT: A 697 LYS cc_start: 0.7124 (mttm) cc_final: 0.6362 (pttp) REVERT: A 772 GLU cc_start: 0.6238 (pm20) cc_final: 0.5728 (mm-30) REVERT: A 814 PHE cc_start: 0.7077 (t80) cc_final: 0.6708 (t80) REVERT: B 709 ASN cc_start: 0.8718 (t0) cc_final: 0.8423 (t0) REVERT: B 772 GLU cc_start: 0.6458 (pt0) cc_final: 0.6174 (mm-30) REVERT: B 1023 MET cc_start: 0.7067 (mmm) cc_final: 0.5993 (mtt) REVERT: B 1188 ILE cc_start: 0.7750 (mm) cc_final: 0.7532 (mm) REVERT: C 440 TYR cc_start: 0.7230 (p90) cc_final: 0.6757 (p90) REVERT: C 460 TRP cc_start: 0.4889 (m100) cc_final: 0.3561 (m100) REVERT: C 467 LEU cc_start: 0.8160 (tp) cc_final: 0.7898 (tt) REVERT: C 657 GLU cc_start: 0.7795 (pt0) cc_final: 0.7217 (tp30) REVERT: C 697 LYS cc_start: 0.7212 (mttm) cc_final: 0.6453 (pttp) REVERT: C 772 GLU cc_start: 0.6325 (pm20) cc_final: 0.5550 (mm-30) REVERT: C 1003 PHE cc_start: 0.4320 (p90) cc_final: 0.3946 (m-80) REVERT: C 1032 TRP cc_start: 0.7997 (m-10) cc_final: 0.7508 (m-10) REVERT: C 1057 MET cc_start: 0.6223 (ttt) cc_final: 0.5743 (ttm) REVERT: C 1098 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6101 (mmt90) REVERT: C 1105 ILE cc_start: 0.8273 (pt) cc_final: 0.7957 (tp) REVERT: C 1128 LYS cc_start: 0.5608 (ttmm) cc_final: 0.4885 (tptp) REVERT: D 500 ILE cc_start: 0.8600 (mm) cc_final: 0.8347 (mm) REVERT: D 508 GLN cc_start: 0.7002 (pm20) cc_final: 0.6151 (tt0) REVERT: D 527 MET cc_start: 0.7945 (tmm) cc_final: 0.7597 (ttp) REVERT: D 713 GLU cc_start: 0.7513 (tt0) cc_final: 0.7035 (tm-30) REVERT: D 772 GLU cc_start: 0.6251 (pt0) cc_final: 0.5919 (mm-30) REVERT: D 1009 MET cc_start: 0.7009 (ptm) cc_final: 0.6681 (ptm) REVERT: D 1023 MET cc_start: 0.7148 (tpt) cc_final: 0.6152 (ttm) REVERT: D 1027 VAL cc_start: 0.8332 (t) cc_final: 0.7986 (m) REVERT: D 1063 TRP cc_start: 0.4344 (m100) cc_final: 0.3886 (m100) REVERT: D 1179 PHE cc_start: 0.8064 (t80) cc_final: 0.7689 (t80) REVERT: D 1188 ILE cc_start: 0.7950 (mm) cc_final: 0.7746 (mm) REVERT: D 1191 MET cc_start: 0.6940 (mtp) cc_final: 0.5589 (tpp) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.2584 time to fit residues: 172.0638 Evaluate side-chains 346 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107579 restraints weight = 39203.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107183 restraints weight = 30842.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108290 restraints weight = 25954.216| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19234 Z= 0.171 Angle : 0.586 8.887 25986 Z= 0.303 Chirality : 0.041 0.212 2908 Planarity : 0.004 0.038 3184 Dihedral : 6.524 83.863 2698 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2362 helix: 1.67 (0.14), residues: 1294 sheet: -1.43 (0.37), residues: 172 loop : -1.43 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1032 HIS 0.005 0.001 HIS C1204 PHE 0.030 0.002 PHE D1096 TYR 0.023 0.001 TYR C1031 ARG 0.005 0.000 ARG C 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.84 seconds wall clock time: 80 minutes 58.11 seconds (4858.11 seconds total)