Starting phenix.real_space_refine on Sun Mar 17 19:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tno_26016/03_2024/7tno_26016_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tno_26016/03_2024/7tno_26016.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/7tno_26016/03_2024/7tno_26016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tno_26016/03_2024/7tno_26016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tno_26016/03_2024/7tno_26016_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tno_26016/03_2024/7tno_26016_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 12198 2.51 5 N 3044 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1203": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1203": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "D ARG 1005": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4667 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "C" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4671 Classifications: {'peptide': 600} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 584} Chain breaks: 4 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.41, per 1000 atoms: 0.50 Number of scatterers: 18810 At special positions: 0 Unit cell: (125.33, 115.37, 136.95, 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 3428 8.00 N 3044 7.00 C 12198 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=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.02 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: 6.79 Conformation dependent library (CDL) restraints added in 3.5 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: 4390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 19 sheets defined 49.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.678A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 625 removed outlier: 3.570A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 641 No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.744A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.514A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.672A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.616A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 821 removed outlier: 3.719A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1028 removed outlier: 3.812A pdb=" N LEU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.907A 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 1105 through 1122 Processing helix chain 'A' and resid 1133 through 1159 removed outlier: 3.617A pdb=" N VAL A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.597A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 removed outlier: 3.872A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.695A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 523 through 544 removed outlier: 3.574A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 598 through 616 removed outlier: 3.552A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.827A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 removed outlier: 4.375A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 removed outlier: 3.505A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 removed outlier: 4.101A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 4.334A pdb=" N VAL B 750 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 755 " --> pdb=" O LYS B 752 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 756 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.502A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 794 through 818 removed outlier: 3.543A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1027 removed outlier: 3.689A pdb=" N LEU B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1103 Processing helix chain 'B' and resid 1105 through 1125 removed outlier: 3.525A pdb=" N CYS B1120 " --> pdb=" O MET B1116 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1159 removed outlier: 3.593A pdb=" N VAL B1154 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1158 " --> pdb=" O VAL B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 removed outlier: 3.517A pdb=" N ILE B1187 " --> pdb=" O ALA B1183 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' 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: 3.805A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 568 Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 622 removed outlier: 3.876A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 675 removed outlier: 3.749A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.592A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 793 through 821 removed outlier: 3.574A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1028 removed outlier: 3.622A pdb=" N THR C1012 " --> pdb=" O GLN C1008 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1103 Processing helix chain 'C' and resid 1105 through 1125 removed outlier: 3.904A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU C1125 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1159 removed outlier: 3.678A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C1158 " --> pdb=" O VAL C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1207 removed outlier: 3.549A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C1189 " --> pdb=" O SER C1185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 removed outlier: 3.570A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.594A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 544 removed outlier: 3.642A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 615 removed outlier: 3.736A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.531A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 620 through 624' Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.581A pdb=" N PHE D 658 " --> pdb=" O SER D 654 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.871A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.614A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.578A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 3.711A pdb=" N ASN D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 765 " --> pdb=" O LYS D 761 " (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 794 through 818 Processing helix chain 'D' and resid 1008 through 1028 Processing helix chain 'D' and resid 1093 through 1102 removed outlier: 3.994A pdb=" N VAL D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1124 removed outlier: 3.592A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1160 removed outlier: 3.554A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D1142 " --> pdb=" O GLY D1138 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D1150 " --> pdb=" O LEU D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1207 removed outlier: 3.531A pdb=" N ILE D1187 " --> pdb=" O ALA D1183 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= B, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.974A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.891A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.582A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1064 through 1067 removed outlier: 3.874A pdb=" N LEU A1075 " --> pdb=" O CYS A1067 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= H, first strand: chain 'B' and resid 496 through 499 removed outlier: 3.916A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.504A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 1173 through 1175 Processing sheet with id= K, first strand: chain 'C' and resid 397 through 399 removed outlier: 3.581A pdb=" N THR C 399 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= M, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.100A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.942A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= P, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= Q, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.686A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.129A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1033 through 1036 removed outlier: 3.515A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS D1066 " --> pdb=" O HIS D1059 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2418 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: 5.02 Time building geometry restraints manager: 7.33 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: 5732 1.34 - 1.47: 4929 1.47 - 1.59: 8338 1.59 - 1.71: 8 1.71 - 1.83: 220 Bond restraints: 19227 Sorted by residual: bond pdb=" N LYS C 449 " pdb=" CA LYS C 449 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.03e+00 bond pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ARG C 453 " pdb=" CA ARG C 453 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.49e+00 bond pdb=" N ASP C 454 " pdb=" CA ASP C 454 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N LYS A 449 " pdb=" CA LYS A 449 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.78e+00 ... (remaining 19222 not shown) Histogram of bond angle deviations from ideal: 93.28 - 101.60: 99 101.60 - 109.92: 2432 109.92 - 118.24: 12171 118.24 - 126.56: 11001 126.56 - 134.89: 272 Bond angle restraints: 25975 Sorted by residual: angle pdb=" C PRO D 507 " pdb=" N GLN D 508 " pdb=" CA GLN D 508 " ideal model delta sigma weight residual 121.54 133.70 -12.16 1.91e+00 2.74e-01 4.05e+01 angle pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta sigma weight residual 121.54 132.92 -11.38 1.91e+00 2.74e-01 3.55e+01 angle pdb=" C ALA D1086 " pdb=" N ASP D1087 " pdb=" CA ASP D1087 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C ARG D1130 " pdb=" N HIS D1131 " pdb=" CA HIS D1131 " ideal model delta sigma weight residual 122.08 129.44 -7.36 1.47e+00 4.63e-01 2.51e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.19e+01 ... (remaining 25970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 10969 24.44 - 48.87: 354 48.87 - 73.31: 24 73.31 - 97.74: 12 97.74 - 122.18: 9 Dihedral angle restraints: 11368 sinusoidal: 4488 harmonic: 6880 Sorted by residual: dihedral pdb=" CA GLN D 508 " pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual 180.00 138.33 41.67 0 5.00e+00 4.00e-02 6.95e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 11365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2321 0.059 - 0.118: 483 0.118 - 0.178: 95 0.178 - 0.237: 7 0.237 - 0.296: 5 Chirality restraints: 2911 Sorted by residual: chirality pdb=" C1 CYZ A1302 " pdb=" C2 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C8 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.79 2.50 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 CYZ D1301 " pdb=" C2 CYZ D1301 " pdb=" C6 CYZ D1301 " pdb=" C8 CYZ D1301 " both_signs ideal model delta sigma weight residual False 2.79 2.51 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C8 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" N2 CYZ C1302 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2908 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 447 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASP C 447 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP C 447 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 448 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 566 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLU D 566 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU D 566 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 567 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 717 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.028 5.00e-02 4.00e+02 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 118 2.60 - 3.17: 15505 3.17 - 3.75: 28712 3.75 - 4.32: 40194 4.32 - 4.90: 64274 Nonbonded interactions: 148803 Sorted by model distance: nonbonded pdb=" OD1 ASP B 760 " pdb="CL CYZ B1302 " model vdw 2.023 3.270 nonbonded pdb=" O PHE B 517 " pdb=" OH TYR B 616 " model vdw 2.302 2.440 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.310 2.440 nonbonded pdb=" O SER B 564 " pdb=" OG1 THR B 568 " model vdw 2.313 2.440 nonbonded pdb=" O PHE D 517 " pdb=" OH TYR D 616 " model vdw 2.315 2.440 ... (remaining 148798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'B' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1041 \ or resid 1056 through 1208 or resid 1302)) selection = (chain 'C' and (resid 394 through 819 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1302)) selection = (chain 'D' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 1041 or resid 1056 through 116 \ 9 or resid 1171 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.460 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 49.690 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.080 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.004 0.060 19227 Z= 0.279 Angle : 0.939 12.405 25975 Z= 0.525 Chirality : 0.051 0.296 2911 Planarity : 0.006 0.058 3188 Dihedral : 12.110 122.178 6942 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.65 % Allowed : 5.24 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -5.12 (0.11), residues: 2362 helix: -3.93 (0.06), residues: 1303 sheet: -2.15 (0.39), residues: 156 loop : -2.42 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A1032 HIS 0.006 0.002 HIS B1081 PHE 0.028 0.002 PHE B1072 TYR 0.028 0.002 TYR B1031 ARG 0.005 0.001 ARG A 692 *********************** 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 724 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 711 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7270 (mtmt) REVERT: A 511 LYS cc_start: 0.6826 (mttp) cc_final: 0.6082 (tptt) REVERT: A 600 ILE cc_start: 0.9378 (mt) cc_final: 0.9124 (mm) REVERT: A 654 SER cc_start: 0.8564 (p) cc_final: 0.8192 (m) REVERT: A 680 SER cc_start: 0.6957 (p) cc_final: 0.6362 (t) REVERT: A 723 VAL cc_start: 0.8267 (m) cc_final: 0.8025 (t) REVERT: A 1030 ASP cc_start: 0.5668 (p0) cc_final: 0.4402 (p0) REVERT: A 1063 TRP cc_start: 0.7834 (m100) cc_final: 0.7435 (m-10) REVERT: A 1130 ARG cc_start: 0.7809 (mmp-170) cc_final: 0.7474 (mmm160) REVERT: A 1147 SER cc_start: 0.8542 (t) cc_final: 0.8316 (p) REVERT: A 1148 ASN cc_start: 0.8342 (t0) cc_final: 0.7951 (t0) REVERT: B 498 LEU cc_start: 0.8853 (pt) cc_final: 0.8584 (pp) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.7887 (t70) REVERT: B 524 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7139 (pt0) REVERT: B 537 SER cc_start: 0.8966 (m) cc_final: 0.8597 (m) REVERT: B 585 MET cc_start: 0.8381 (mmt) cc_final: 0.8166 (mmm) REVERT: B 620 LEU cc_start: 0.8065 (tp) cc_final: 0.7752 (tp) REVERT: B 661 ARG cc_start: 0.5955 (mmp80) cc_final: 0.5689 (ptp90) REVERT: B 1021 SER cc_start: 0.8411 (m) cc_final: 0.8102 (p) REVERT: B 1022 LEU cc_start: 0.8408 (mt) cc_final: 0.8193 (mp) REVERT: B 1148 ASN cc_start: 0.8770 (t0) cc_final: 0.8553 (t0) REVERT: B 1187 ILE cc_start: 0.9218 (mt) cc_final: 0.8990 (mt) REVERT: C 438 PHE cc_start: 0.5883 (p90) cc_final: 0.5582 (p90) REVERT: C 460 TRP cc_start: 0.5889 (m100) cc_final: 0.5576 (m100) REVERT: C 498 LEU cc_start: 0.8354 (pp) cc_final: 0.7740 (pp) REVERT: C 501 SER cc_start: 0.8390 (p) cc_final: 0.8086 (t) REVERT: C 683 VAL cc_start: 0.7310 (m) cc_final: 0.6873 (m) REVERT: C 699 LYS cc_start: 0.8011 (mptt) cc_final: 0.7675 (mmmt) REVERT: C 711 TYR cc_start: 0.7413 (t80) cc_final: 0.7211 (t80) REVERT: C 732 TYR cc_start: 0.7976 (m-10) cc_final: 0.7639 (m-10) REVERT: C 764 ASN cc_start: 0.7857 (m-40) cc_final: 0.7571 (t0) REVERT: C 817 LYS cc_start: 0.7905 (mmpt) cc_final: 0.7644 (mmmt) REVERT: C 1031 TYR cc_start: 0.3906 (p90) cc_final: 0.3598 (p90) REVERT: C 1036 ARG cc_start: 0.6959 (mmt180) cc_final: 0.6704 (mmt-90) REVERT: C 1096 PHE cc_start: 0.7793 (t80) cc_final: 0.7495 (t80) REVERT: C 1120 CYS cc_start: 0.7700 (m) cc_final: 0.7256 (m) REVERT: C 1126 PHE cc_start: 0.6414 (m-10) cc_final: 0.5863 (m-80) REVERT: C 1169 LYS cc_start: 0.2793 (tptp) cc_final: 0.1150 (ptmt) REVERT: D 425 CYS cc_start: 0.7947 (m) cc_final: 0.7681 (m) REVERT: D 476 ILE cc_start: 0.8670 (mt) cc_final: 0.8432 (mp) REVERT: D 533 TYR cc_start: 0.8753 (t80) cc_final: 0.8484 (t80) REVERT: D 637 GLU cc_start: 0.8196 (pp20) cc_final: 0.7684 (pp20) REVERT: D 639 LEU cc_start: 0.7958 (tp) cc_final: 0.7574 (tp) REVERT: D 720 THR cc_start: 0.8009 (p) cc_final: 0.7643 (p) REVERT: D 764 ASN cc_start: 0.7839 (p0) cc_final: 0.7545 (p0) REVERT: D 770 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6659 (mmtt) REVERT: D 1170 LYS cc_start: 0.5128 (tptp) cc_final: 0.4853 (ptpp) REVERT: D 1173 TYR cc_start: 0.6761 (p90) cc_final: 0.6477 (p90) outliers start: 13 outliers final: 2 residues processed: 721 average time/residue: 0.3151 time to fit residues: 336.6859 Evaluate side-chains 426 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 423 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 0.0070 chunk 188 optimal weight: 0.0000 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 6.9990 overall best weight: 1.7606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 619 ASN A1204 HIS B 411 ASN B 587 GLN B 791 ASN B1008 GLN B1131 HIS B1204 HIS C1059 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN D 791 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** D1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS D1206 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19227 Z= 0.249 Angle : 0.634 12.285 25975 Z= 0.336 Chirality : 0.042 0.215 2911 Planarity : 0.005 0.065 3188 Dihedral : 9.185 108.190 2697 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 0.20 % Allowed : 3.79 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -2.46 (0.14), residues: 2362 helix: -1.15 (0.12), residues: 1290 sheet: -1.90 (0.37), residues: 181 loop : -2.12 (0.17), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 460 HIS 0.005 0.001 HIS B1081 PHE 0.022 0.002 PHE D 574 TYR 0.024 0.002 TYR C1031 ARG 0.005 0.001 ARG D 594 *********************** 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 495 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 491 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7910 (mt) cc_final: 0.7611 (pt) REVERT: A 450 TYR cc_start: 0.7095 (m-80) cc_final: 0.6696 (m-80) REVERT: A 487 GLU cc_start: 0.7639 (tp30) cc_final: 0.7160 (pt0) REVERT: A 511 LYS cc_start: 0.6979 (mttp) cc_final: 0.6298 (tptt) REVERT: A 600 ILE cc_start: 0.9323 (mt) cc_final: 0.9025 (mm) REVERT: A 732 TYR cc_start: 0.7871 (m-10) cc_final: 0.7280 (m-80) REVERT: A 1063 TRP cc_start: 0.7898 (m100) cc_final: 0.7478 (m-10) REVERT: A 1130 ARG cc_start: 0.7927 (mmp-170) cc_final: 0.7455 (mmm160) REVERT: A 1148 ASN cc_start: 0.8237 (t0) cc_final: 0.8033 (t0) REVERT: A 1199 MET cc_start: 0.7696 (mmm) cc_final: 0.7416 (mmt) REVERT: B 1008 GLN cc_start: 0.7214 (pt0) cc_final: 0.6788 (pt0) REVERT: B 1021 SER cc_start: 0.8504 (m) cc_final: 0.8214 (p) REVERT: B 1023 MET cc_start: 0.8433 (tpp) cc_final: 0.7876 (tpt) REVERT: B 1148 ASN cc_start: 0.8960 (t0) cc_final: 0.8747 (t0) REVERT: C 400 ILE cc_start: 0.9012 (tp) cc_final: 0.8709 (tp) REVERT: C 438 PHE cc_start: 0.6171 (p90) cc_final: 0.5700 (p90) REVERT: C 497 SER cc_start: 0.8364 (t) cc_final: 0.7936 (m) REVERT: C 711 TYR cc_start: 0.7618 (t80) cc_final: 0.7378 (t80) REVERT: C 732 TYR cc_start: 0.7833 (m-10) cc_final: 0.7429 (m-10) REVERT: C 817 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7635 (mmmt) REVERT: C 1010 LEU cc_start: 0.7961 (mm) cc_final: 0.7749 (mp) REVERT: C 1020 PHE cc_start: 0.8118 (t80) cc_final: 0.7831 (t80) REVERT: C 1031 TYR cc_start: 0.4805 (p90) cc_final: 0.3819 (p90) REVERT: C 1092 THR cc_start: 0.6849 (p) cc_final: 0.6589 (t) REVERT: C 1152 ILE cc_start: 0.8622 (mt) cc_final: 0.8410 (mt) REVERT: C 1156 ILE cc_start: 0.8839 (mt) cc_final: 0.8621 (mp) REVERT: C 1169 LYS cc_start: 0.3040 (tptp) cc_final: 0.1427 (ptmt) REVERT: D 425 CYS cc_start: 0.7907 (m) cc_final: 0.7460 (m) REVERT: D 1139 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8263 (tt) outliers start: 4 outliers final: 0 residues processed: 493 average time/residue: 0.2880 time to fit residues: 215.9561 Evaluate side-chains 362 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN B1204 HIS C1059 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 726 ASN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** D1159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19227 Z= 0.210 Angle : 0.590 10.235 25975 Z= 0.307 Chirality : 0.041 0.242 2911 Planarity : 0.004 0.046 3188 Dihedral : 8.430 100.475 2697 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 0.15 % Allowed : 4.29 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.12 (0.16), residues: 2362 helix: 0.24 (0.14), residues: 1287 sheet: -1.81 (0.38), residues: 161 loop : -1.93 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 460 HIS 0.008 0.001 HIS B1204 PHE 0.022 0.002 PHE C1200 TYR 0.020 0.001 TYR A 647 ARG 0.005 0.000 ARG D 594 *********************** 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 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 457 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7848 (mt) cc_final: 0.7499 (pt) REVERT: A 425 CYS cc_start: 0.8296 (p) cc_final: 0.7949 (p) REVERT: A 487 GLU cc_start: 0.7619 (tp30) cc_final: 0.7163 (pt0) REVERT: A 511 LYS cc_start: 0.6968 (mttp) cc_final: 0.6273 (tptt) REVERT: A 600 ILE cc_start: 0.9302 (mt) cc_final: 0.9001 (mm) REVERT: A 671 TRP cc_start: 0.7815 (t-100) cc_final: 0.7548 (t-100) REVERT: A 1008 GLN cc_start: 0.7907 (pt0) cc_final: 0.7494 (pt0) REVERT: A 1063 TRP cc_start: 0.7775 (m100) cc_final: 0.7437 (m-10) REVERT: A 1130 ARG cc_start: 0.7998 (mmp-170) cc_final: 0.7602 (mmm160) REVERT: A 1199 MET cc_start: 0.7647 (mmm) cc_final: 0.7220 (tpp) REVERT: B 651 ASP cc_start: 0.5803 (t0) cc_final: 0.4452 (p0) REVERT: B 752 LYS cc_start: 0.8063 (mttt) cc_final: 0.7770 (mptt) REVERT: B 776 LYS cc_start: 0.4268 (tttt) cc_final: 0.4044 (tttm) REVERT: B 1021 SER cc_start: 0.8446 (m) cc_final: 0.8153 (p) REVERT: B 1023 MET cc_start: 0.8408 (tpp) cc_final: 0.7826 (tpt) REVERT: B 1148 ASN cc_start: 0.8932 (t0) cc_final: 0.8664 (t0) REVERT: C 438 PHE cc_start: 0.6106 (p90) cc_final: 0.5512 (p90) REVERT: C 483 LEU cc_start: 0.7682 (tp) cc_final: 0.7031 (tp) REVERT: C 501 SER cc_start: 0.8053 (p) cc_final: 0.7764 (t) REVERT: C 585 MET cc_start: 0.8719 (mmm) cc_final: 0.8433 (mmm) REVERT: C 817 LYS cc_start: 0.8004 (mmpt) cc_final: 0.7667 (mmmt) REVERT: C 1020 PHE cc_start: 0.8075 (t80) cc_final: 0.7830 (t80) REVERT: C 1031 TYR cc_start: 0.4217 (p90) cc_final: 0.3471 (p90) REVERT: C 1072 PHE cc_start: 0.5941 (m-10) cc_final: 0.5700 (m-80) REVERT: C 1075 LEU cc_start: 0.6334 (mm) cc_final: 0.5470 (tp) REVERT: C 1092 THR cc_start: 0.6994 (p) cc_final: 0.6790 (t) REVERT: C 1156 ILE cc_start: 0.8850 (mt) cc_final: 0.8634 (mp) REVERT: C 1169 LYS cc_start: 0.2886 (tptp) cc_final: 0.1357 (ptmt) REVERT: D 425 CYS cc_start: 0.7763 (m) cc_final: 0.7337 (m) REVERT: D 533 TYR cc_start: 0.8891 (t80) cc_final: 0.8537 (t80) REVERT: D 580 SER cc_start: 0.9392 (m) cc_final: 0.8897 (p) REVERT: D 713 GLU cc_start: 0.7223 (tt0) cc_final: 0.6745 (tp30) REVERT: D 1139 ILE cc_start: 0.8660 (mp) cc_final: 0.8322 (tt) outliers start: 3 outliers final: 0 residues processed: 459 average time/residue: 0.2869 time to fit residues: 203.1779 Evaluate side-chains 346 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 435 HIS D 508 GLN D 726 ASN ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 ASN D1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19227 Z= 0.358 Angle : 0.695 10.255 25975 Z= 0.363 Chirality : 0.045 0.298 2911 Planarity : 0.005 0.071 3188 Dihedral : 8.453 100.516 2697 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.91 (0.16), residues: 2362 helix: 0.51 (0.14), residues: 1282 sheet: -2.20 (0.41), residues: 138 loop : -1.90 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 460 HIS 0.007 0.002 HIS D 435 PHE 0.023 0.002 PHE C 546 TYR 0.028 0.002 TYR B1031 ARG 0.004 0.001 ARG B 594 *********************** 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 439 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 437 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7896 (mt) cc_final: 0.7597 (pt) REVERT: A 425 CYS cc_start: 0.8367 (p) cc_final: 0.8055 (p) REVERT: A 511 LYS cc_start: 0.6995 (mttp) cc_final: 0.6315 (tptt) REVERT: A 600 ILE cc_start: 0.9302 (mt) cc_final: 0.9025 (mm) REVERT: A 1157 SER cc_start: 0.8800 (p) cc_final: 0.8598 (p) REVERT: B 431 GLU cc_start: 0.7836 (tp30) cc_final: 0.7212 (tp30) REVERT: B 585 MET cc_start: 0.8396 (mmm) cc_final: 0.7914 (mtt) REVERT: B 620 LEU cc_start: 0.8031 (tp) cc_final: 0.7828 (tp) REVERT: B 1021 SER cc_start: 0.8505 (m) cc_final: 0.8232 (p) REVERT: B 1023 MET cc_start: 0.8458 (tpp) cc_final: 0.7855 (tpt) REVERT: B 1148 ASN cc_start: 0.8970 (t0) cc_final: 0.8747 (t0) REVERT: C 438 PHE cc_start: 0.6387 (p90) cc_final: 0.5847 (p90) REVERT: C 501 SER cc_start: 0.8254 (p) cc_final: 0.7928 (t) REVERT: C 671 TRP cc_start: 0.6755 (t-100) cc_final: 0.6547 (t-100) REVERT: C 708 MET cc_start: 0.7602 (mmt) cc_final: 0.7376 (mmm) REVERT: C 817 LYS cc_start: 0.7992 (mmpt) cc_final: 0.7641 (mmmt) REVERT: C 1020 PHE cc_start: 0.8134 (t80) cc_final: 0.7850 (t80) REVERT: C 1156 ILE cc_start: 0.8805 (mt) cc_final: 0.8599 (mp) REVERT: D 414 MET cc_start: 0.7897 (mtm) cc_final: 0.7534 (mtm) REVERT: D 425 CYS cc_start: 0.7786 (m) cc_final: 0.7503 (m) REVERT: D 533 TYR cc_start: 0.8979 (t80) cc_final: 0.8697 (t80) REVERT: D 580 SER cc_start: 0.9441 (m) cc_final: 0.8919 (p) REVERT: D 671 TRP cc_start: 0.7578 (t-100) cc_final: 0.7278 (t-100) REVERT: D 1139 ILE cc_start: 0.8592 (mp) cc_final: 0.8282 (tt) outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 0.2808 time to fit residues: 189.8650 Evaluate side-chains 329 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN C1059 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19227 Z= 0.162 Angle : 0.575 10.939 25975 Z= 0.295 Chirality : 0.040 0.266 2911 Planarity : 0.004 0.067 3188 Dihedral : 7.448 89.515 2697 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2362 helix: 1.13 (0.14), residues: 1288 sheet: -1.92 (0.44), residues: 133 loop : -1.68 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 460 HIS 0.007 0.001 HIS B1204 PHE 0.025 0.001 PHE B1200 TYR 0.019 0.001 TYR C 732 ARG 0.006 0.000 ARG C 453 *********************** 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 465 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7816 (mt) cc_final: 0.7497 (pt) REVERT: A 425 CYS cc_start: 0.8081 (p) cc_final: 0.7786 (p) REVERT: A 476 ILE cc_start: 0.9094 (mt) cc_final: 0.8646 (pt) REVERT: A 487 GLU cc_start: 0.7634 (tp30) cc_final: 0.7036 (pt0) REVERT: A 511 LYS cc_start: 0.6939 (mttp) cc_final: 0.6272 (tptt) REVERT: A 670 MET cc_start: 0.7420 (mmt) cc_final: 0.7065 (mmt) REVERT: A 1063 TRP cc_start: 0.7679 (m100) cc_final: 0.7382 (m-10) REVERT: A 1130 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7556 (mmt-90) REVERT: B 752 LYS cc_start: 0.8089 (mttt) cc_final: 0.7756 (mptt) REVERT: B 1021 SER cc_start: 0.8355 (m) cc_final: 0.8011 (p) REVERT: B 1023 MET cc_start: 0.8422 (tpp) cc_final: 0.7913 (tpt) REVERT: B 1032 TRP cc_start: 0.7359 (m100) cc_final: 0.7079 (m-10) REVERT: B 1148 ASN cc_start: 0.8848 (t0) cc_final: 0.8631 (t0) REVERT: B 1156 ILE cc_start: 0.8617 (mt) cc_final: 0.8123 (mt) REVERT: C 438 PHE cc_start: 0.6042 (p90) cc_final: 0.5467 (p90) REVERT: C 483 LEU cc_start: 0.7763 (tp) cc_final: 0.7244 (tp) REVERT: C 501 SER cc_start: 0.8207 (p) cc_final: 0.7865 (t) REVERT: C 674 MET cc_start: 0.6181 (mpp) cc_final: 0.5569 (mpp) REVERT: C 708 MET cc_start: 0.7446 (mmt) cc_final: 0.7237 (mmm) REVERT: C 711 TYR cc_start: 0.7868 (t80) cc_final: 0.7563 (t80) REVERT: C 817 LYS cc_start: 0.8019 (mmpt) cc_final: 0.7650 (mmmt) REVERT: C 1036 ARG cc_start: 0.6667 (mmt90) cc_final: 0.6098 (ttm-80) REVERT: C 1108 ILE cc_start: 0.8472 (mm) cc_final: 0.8269 (mm) REVERT: C 1156 ILE cc_start: 0.8820 (mt) cc_final: 0.8542 (mp) REVERT: D 414 MET cc_start: 0.7926 (mtm) cc_final: 0.7541 (mtm) REVERT: D 425 CYS cc_start: 0.7855 (m) cc_final: 0.7504 (m) REVERT: D 580 SER cc_start: 0.9340 (m) cc_final: 0.8755 (p) REVERT: D 1139 ILE cc_start: 0.8546 (mp) cc_final: 0.8278 (tt) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.2889 time to fit residues: 214.4478 Evaluate side-chains 350 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0570 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19227 Z= 0.264 Angle : 0.633 13.136 25975 Z= 0.329 Chirality : 0.043 0.273 2911 Planarity : 0.004 0.067 3188 Dihedral : 7.382 94.397 2697 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2362 helix: 1.12 (0.14), residues: 1280 sheet: -2.03 (0.43), residues: 138 loop : -1.71 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 460 HIS 0.010 0.002 HIS B1204 PHE 0.024 0.002 PHE C1200 TYR 0.022 0.002 TYR B1031 ARG 0.004 0.000 ARG D1005 *********************** 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 432 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8136 (p) cc_final: 0.7838 (p) REVERT: A 487 GLU cc_start: 0.7632 (tp30) cc_final: 0.7007 (pt0) REVERT: A 511 LYS cc_start: 0.6965 (mttp) cc_final: 0.6328 (tptt) REVERT: A 600 ILE cc_start: 0.9276 (mt) cc_final: 0.8896 (mm) REVERT: B 713 GLU cc_start: 0.7144 (tt0) cc_final: 0.6868 (tt0) REVERT: B 1021 SER cc_start: 0.8390 (m) cc_final: 0.8090 (p) REVERT: B 1023 MET cc_start: 0.8459 (tpp) cc_final: 0.7847 (tpt) REVERT: B 1065 THR cc_start: 0.7164 (t) cc_final: 0.6423 (m) REVERT: B 1148 ASN cc_start: 0.8907 (t0) cc_final: 0.8666 (t0) REVERT: C 438 PHE cc_start: 0.6153 (p90) cc_final: 0.5677 (p90) REVERT: C 497 SER cc_start: 0.8536 (t) cc_final: 0.8153 (m) REVERT: C 501 SER cc_start: 0.8226 (p) cc_final: 0.7871 (t) REVERT: C 674 MET cc_start: 0.6259 (mpp) cc_final: 0.5649 (mpp) REVERT: C 1020 PHE cc_start: 0.8070 (t80) cc_final: 0.7755 (t80) REVERT: C 1156 ILE cc_start: 0.8736 (mt) cc_final: 0.8498 (mp) REVERT: D 580 SER cc_start: 0.9427 (m) cc_final: 0.8883 (p) REVERT: D 816 TYR cc_start: 0.6297 (t80) cc_final: 0.6057 (t80) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2688 time to fit residues: 182.3994 Evaluate side-chains 338 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19227 Z= 0.185 Angle : 0.584 14.021 25975 Z= 0.299 Chirality : 0.041 0.228 2911 Planarity : 0.004 0.072 3188 Dihedral : 6.839 91.029 2697 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2362 helix: 1.33 (0.15), residues: 1298 sheet: -1.89 (0.45), residues: 133 loop : -1.68 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 460 HIS 0.008 0.001 HIS A1059 PHE 0.024 0.001 PHE C1200 TYR 0.019 0.001 TYR A 533 ARG 0.003 0.000 ARG D1005 *********************** 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 441 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 CYS cc_start: 0.8136 (p) cc_final: 0.7819 (p) REVERT: A 487 GLU cc_start: 0.7504 (tp30) cc_final: 0.7038 (pt0) REVERT: A 511 LYS cc_start: 0.6912 (mttp) cc_final: 0.6310 (tptt) REVERT: A 600 ILE cc_start: 0.9250 (mt) cc_final: 0.8920 (mm) REVERT: A 629 MET cc_start: 0.4139 (mpp) cc_final: 0.3448 (tpt) REVERT: A 633 ILE cc_start: 0.7340 (mm) cc_final: 0.6627 (mm) REVERT: A 674 MET cc_start: 0.7156 (mmt) cc_final: 0.6838 (mmt) REVERT: A 705 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 1063 TRP cc_start: 0.7539 (m100) cc_final: 0.7315 (m-10) REVERT: B 713 GLU cc_start: 0.7229 (tt0) cc_final: 0.6913 (tt0) REVERT: B 721 MET cc_start: 0.7048 (mtm) cc_final: 0.6838 (mtp) REVERT: B 752 LYS cc_start: 0.8062 (mttt) cc_final: 0.7773 (mptt) REVERT: B 1023 MET cc_start: 0.8421 (tpp) cc_final: 0.7945 (tpt) REVERT: B 1065 THR cc_start: 0.7148 (t) cc_final: 0.6279 (m) REVERT: C 438 PHE cc_start: 0.6111 (p90) cc_final: 0.5626 (p90) REVERT: C 483 LEU cc_start: 0.7767 (tp) cc_final: 0.7207 (tp) REVERT: C 497 SER cc_start: 0.8463 (t) cc_final: 0.8233 (m) REVERT: C 501 SER cc_start: 0.8340 (p) cc_final: 0.7943 (t) REVERT: C 674 MET cc_start: 0.6139 (mpp) cc_final: 0.5508 (mpp) REVERT: C 1020 PHE cc_start: 0.8041 (t80) cc_final: 0.7751 (t80) REVERT: C 1156 ILE cc_start: 0.8712 (mt) cc_final: 0.8474 (mp) REVERT: D 425 CYS cc_start: 0.7864 (m) cc_final: 0.7466 (m) REVERT: D 580 SER cc_start: 0.9361 (m) cc_final: 0.8754 (p) REVERT: D 644 GLU cc_start: 0.7232 (mp0) cc_final: 0.6300 (tm-30) REVERT: D 645 ILE cc_start: 0.7735 (mt) cc_final: 0.7471 (mt) REVERT: D 727 LEU cc_start: 0.9016 (mt) cc_final: 0.8730 (mt) REVERT: A 1301 GLU cc_start: 0.6311 (tp30) cc_final: 0.4482 (mm-30) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2733 time to fit residues: 188.2000 Evaluate side-chains 336 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN A 619 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19227 Z= 0.183 Angle : 0.586 11.633 25975 Z= 0.299 Chirality : 0.041 0.235 2911 Planarity : 0.004 0.072 3188 Dihedral : 6.664 89.464 2697 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2362 helix: 1.46 (0.15), residues: 1289 sheet: -1.75 (0.46), residues: 133 loop : -1.67 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 460 HIS 0.005 0.001 HIS D1059 PHE 0.027 0.001 PHE C1200 TYR 0.016 0.001 TYR C 732 ARG 0.003 0.000 ARG A 453 *********************** 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 432 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 GLU cc_start: 0.7442 (tp30) cc_final: 0.7036 (pt0) REVERT: A 511 LYS cc_start: 0.6939 (mttp) cc_final: 0.6328 (tptt) REVERT: A 600 ILE cc_start: 0.9258 (mt) cc_final: 0.8905 (mm) REVERT: A 629 MET cc_start: 0.3933 (mpp) cc_final: 0.3191 (tpt) REVERT: A 674 MET cc_start: 0.7265 (mmt) cc_final: 0.6983 (mmt) REVERT: A 1063 TRP cc_start: 0.7598 (m100) cc_final: 0.7359 (m-10) REVERT: B 713 GLU cc_start: 0.7205 (tt0) cc_final: 0.6915 (tt0) REVERT: B 752 LYS cc_start: 0.8067 (mttt) cc_final: 0.7748 (mptt) REVERT: B 1021 SER cc_start: 0.8332 (m) cc_final: 0.8011 (p) REVERT: B 1065 THR cc_start: 0.7143 (t) cc_final: 0.6283 (m) REVERT: C 438 PHE cc_start: 0.5994 (p90) cc_final: 0.5488 (p90) REVERT: C 483 LEU cc_start: 0.7713 (tp) cc_final: 0.7210 (tp) REVERT: C 497 SER cc_start: 0.8580 (t) cc_final: 0.8372 (m) REVERT: C 501 SER cc_start: 0.8271 (p) cc_final: 0.7890 (t) REVERT: C 674 MET cc_start: 0.6127 (mpp) cc_final: 0.5476 (mpp) REVERT: C 817 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7666 (mmmt) REVERT: C 1020 PHE cc_start: 0.8044 (t80) cc_final: 0.7760 (t80) REVERT: C 1156 ILE cc_start: 0.8696 (mt) cc_final: 0.8471 (mp) REVERT: D 425 CYS cc_start: 0.7858 (m) cc_final: 0.7474 (m) REVERT: D 580 SER cc_start: 0.9380 (m) cc_final: 0.8769 (p) REVERT: D 644 GLU cc_start: 0.7372 (mp0) cc_final: 0.6754 (tt0) REVERT: D 713 GLU cc_start: 0.7103 (tt0) cc_final: 0.6646 (tp30) REVERT: D 727 LEU cc_start: 0.9013 (mt) cc_final: 0.8724 (mt) REVERT: D 752 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7860 (ttmm) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2716 time to fit residues: 184.2914 Evaluate side-chains 339 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 0.4980 chunk 215 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 169 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 194 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 HIS D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19227 Z= 0.144 Angle : 0.569 13.385 25975 Z= 0.288 Chirality : 0.040 0.254 2911 Planarity : 0.004 0.060 3188 Dihedral : 6.201 83.853 2697 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.17), residues: 2362 helix: 1.60 (0.15), residues: 1309 sheet: -1.68 (0.46), residues: 133 loop : -1.67 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 671 HIS 0.005 0.001 HIS C 435 PHE 0.027 0.001 PHE C1200 TYR 0.019 0.001 TYR A 533 ARG 0.005 0.000 ARG D 692 *********************** 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 436 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.7945 (mmt) cc_final: 0.7691 (mmt) REVERT: A 511 LYS cc_start: 0.6823 (mttp) cc_final: 0.6223 (tptt) REVERT: A 600 ILE cc_start: 0.9227 (mt) cc_final: 0.8850 (mm) REVERT: A 629 MET cc_start: 0.3953 (mpp) cc_final: 0.3199 (tpt) REVERT: A 674 MET cc_start: 0.7303 (mmt) cc_final: 0.7026 (mmt) REVERT: A 705 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 1063 TRP cc_start: 0.7538 (m100) cc_final: 0.7315 (m-10) REVERT: B 752 LYS cc_start: 0.8043 (mttt) cc_final: 0.7772 (mptt) REVERT: B 1021 SER cc_start: 0.8291 (m) cc_final: 0.8014 (p) REVERT: B 1032 TRP cc_start: 0.7724 (m100) cc_final: 0.7225 (m-10) REVERT: B 1115 PHE cc_start: 0.6964 (t80) cc_final: 0.6246 (t80) REVERT: C 483 LEU cc_start: 0.7754 (tp) cc_final: 0.7169 (tp) REVERT: C 497 SER cc_start: 0.8569 (t) cc_final: 0.8360 (m) REVERT: C 501 SER cc_start: 0.8279 (p) cc_final: 0.7875 (t) REVERT: C 674 MET cc_start: 0.6163 (mpp) cc_final: 0.5406 (mpp) REVERT: C 817 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7689 (mmmt) REVERT: C 1020 PHE cc_start: 0.8029 (t80) cc_final: 0.7760 (t80) REVERT: C 1031 TYR cc_start: 0.3950 (p90) cc_final: 0.3485 (p90) REVERT: C 1156 ILE cc_start: 0.8692 (mt) cc_final: 0.8475 (mp) REVERT: D 425 CYS cc_start: 0.7893 (m) cc_final: 0.7510 (m) REVERT: D 580 SER cc_start: 0.9253 (m) cc_final: 0.8592 (p) REVERT: D 629 MET cc_start: 0.7417 (ppp) cc_final: 0.6462 (mtp) REVERT: D 644 GLU cc_start: 0.7513 (mp0) cc_final: 0.6714 (tt0) REVERT: D 713 GLU cc_start: 0.7021 (tt0) cc_final: 0.6538 (tp30) REVERT: D 727 LEU cc_start: 0.9016 (mt) cc_final: 0.8689 (mt) REVERT: D 752 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7906 (ttmm) REVERT: A 1301 GLU cc_start: 0.6198 (tp30) cc_final: 0.4638 (mm-30) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2819 time to fit residues: 191.6587 Evaluate side-chains 338 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 ASN B1204 HIS ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19227 Z= 0.395 Angle : 0.749 14.976 25975 Z= 0.387 Chirality : 0.047 0.271 2911 Planarity : 0.005 0.069 3188 Dihedral : 7.219 98.043 2697 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2362 helix: 0.98 (0.14), residues: 1280 sheet: -1.88 (0.46), residues: 133 loop : -1.80 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 460 HIS 0.008 0.002 HIS C1059 PHE 0.030 0.002 PHE C1200 TYR 0.029 0.002 TYR B1031 ARG 0.007 0.001 ARG B 420 ********************** 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 396 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 511 LYS cc_start: 0.6967 (mttp) cc_final: 0.6380 (tptt) REVERT: A 600 ILE cc_start: 0.9355 (mt) cc_final: 0.9020 (mm) REVERT: A 629 MET cc_start: 0.4193 (mpp) cc_final: 0.3321 (tpt) REVERT: A 674 MET cc_start: 0.7243 (mmt) cc_final: 0.6957 (mmt) REVERT: A 1157 SER cc_start: 0.8851 (p) cc_final: 0.8637 (p) REVERT: B 503 MET cc_start: 0.8334 (ptm) cc_final: 0.8032 (ptm) REVERT: B 705 GLU cc_start: 0.7407 (mp0) cc_final: 0.7140 (mm-30) REVERT: B 713 GLU cc_start: 0.7361 (tt0) cc_final: 0.7144 (tt0) REVERT: B 721 MET cc_start: 0.7666 (mtm) cc_final: 0.7313 (mtp) REVERT: B 1008 GLN cc_start: 0.7574 (pt0) cc_final: 0.7345 (pt0) REVERT: B 1023 MET cc_start: 0.8521 (tpt) cc_final: 0.7828 (tpt) REVERT: B 1065 THR cc_start: 0.7318 (t) cc_final: 0.6600 (m) REVERT: B 1115 PHE cc_start: 0.6803 (t80) cc_final: 0.6207 (t80) REVERT: C 438 PHE cc_start: 0.6332 (p90) cc_final: 0.5980 (p90) REVERT: C 501 SER cc_start: 0.8347 (p) cc_final: 0.8030 (t) REVERT: C 527 MET cc_start: 0.8217 (ttm) cc_final: 0.7950 (ttm) REVERT: C 629 MET cc_start: 0.4290 (tmm) cc_final: 0.4079 (tmm) REVERT: C 674 MET cc_start: 0.6240 (mpp) cc_final: 0.5360 (mpp) REVERT: C 682 PHE cc_start: 0.5306 (m-80) cc_final: 0.5009 (m-80) REVERT: C 1020 PHE cc_start: 0.8032 (t80) cc_final: 0.7665 (t80) REVERT: C 1082 PHE cc_start: 0.7272 (p90) cc_final: 0.6993 (p90) REVERT: C 1156 ILE cc_start: 0.8838 (mt) cc_final: 0.8631 (mp) REVERT: D 580 SER cc_start: 0.9417 (m) cc_final: 0.8899 (p) REVERT: D 629 MET cc_start: 0.7601 (ppp) cc_final: 0.6649 (mtp) REVERT: D 644 GLU cc_start: 0.7542 (mp0) cc_final: 0.6862 (tt0) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2638 time to fit residues: 165.2297 Evaluate side-chains 304 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.0670 chunk 202 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 714 GLN B1159 ASN ** C1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104840 restraints weight = 39588.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105745 restraints weight = 24765.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105854 restraints weight = 19346.235| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19227 Z= 0.162 Angle : 0.609 14.543 25975 Z= 0.307 Chirality : 0.041 0.247 2911 Planarity : 0.004 0.086 3188 Dihedral : 6.534 89.726 2697 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2362 helix: 1.39 (0.15), residues: 1305 sheet: -1.58 (0.47), residues: 132 loop : -1.72 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 671 HIS 0.005 0.001 HIS A1204 PHE 0.028 0.001 PHE C1200 TYR 0.023 0.001 TYR C 732 ARG 0.006 0.000 ARG C 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.38 seconds wall clock time: 79 minutes 38.01 seconds (4778.01 seconds total)