Starting phenix.real_space_refine on Tue Feb 20 13:30:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gfw_4397/02_2024/6gfw_4397_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 P 103 5.49 5 S 93 5.16 5 C 17192 2.51 5 N 4997 2.21 5 O 5620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 452": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1171": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1301": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 901": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1194": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1371": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "M GLU 356": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28005 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1763 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 9998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 9998 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 596 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 16, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 397 Chain: "D" Number of atoms: 9722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 9722 Classifications: {'peptide': 1345} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1291} Chain breaks: 4 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 652 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 12, 'GLU:plan': 32, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 497 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1026 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2102 Classifications: {'peptide': 366} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 227} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 353} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 1000 Unresolved non-hydrogen dihedrals: 608 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 2, 'UNK:plan-1': 49, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 474 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 14.31, per 1000 atoms: 0.51 Number of scatterers: 28005 At special positions: 0 Unit cell: (138.24, 171.72, 165.24, 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) S 93 16.00 P 103 15.00 O 5620 8.00 N 4997 7.00 C 17192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 11.16 Conformation dependent library (CDL) restraints added in 4.9 seconds 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6674 Finding SS restraints... Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC G 5 Was trying to link: DC G 5 O2 with DG F -5 N1, Saenger class: 22 Secondary structure from input PDB file: 119 helices and 40 sheets defined 38.1% alpha, 11.6% beta 30 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 8.98 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 4.258A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.889A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.886A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.845A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.985A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.904A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.037A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.648A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 235' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.595A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.955A pdb=" N ALA C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.572A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 329 removed outlier: 4.165A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.761A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.090A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.155A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.792A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.739A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.602A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.868A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.087A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.707A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.506A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.924A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 982 removed outlier: 3.752A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.572A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.612A pdb=" N ARG C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 removed outlier: 3.589A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.336A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.995A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1177 Processing helix chain 'C' and resid 1191 through 1201 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.580A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 4.003A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.558A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.895A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.681A pdb=" N GLY D 73 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.773A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 99' Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 182 through 191 removed outlier: 4.247A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.570A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 3.816A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.765A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 284 removed outlier: 4.183A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.667A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.625A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 4.063A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.583A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.834A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.537A pdb=" N SER D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 3.994A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 787 removed outlier: 4.348A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 804 removed outlier: 4.115A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.164A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 917 through 925 removed outlier: 5.465A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.546A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.383A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1312 through 1316 removed outlier: 3.552A pdb=" N THR D1316 " --> pdb=" O SER D1313 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 4.104A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1374 removed outlier: 3.807A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 4.136A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.229A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.527A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 123 through 130 removed outlier: 3.691A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 147 removed outlier: 4.285A pdb=" N ALA M 139 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 removed outlier: 4.335A pdb=" N GLY M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 186 removed outlier: 3.963A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE M 185 " --> pdb=" O ARG M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 removed outlier: 4.530A pdb=" N LEU M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 223 removed outlier: 4.261A pdb=" N ILE M 219 " --> pdb=" O GLU M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 4.352A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 245 Processing helix chain 'M' and resid 246 through 255 removed outlier: 3.809A pdb=" N SER M 255 " --> pdb=" O ASN M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.813A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA M 310 " --> pdb=" O MET M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 355 removed outlier: 3.651A pdb=" N ALA M 326 " --> pdb=" O ASN M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.657A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.609A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 404 removed outlier: 3.513A pdb=" N UNK M 403 " --> pdb=" O UNK M 400 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N UNK M 404 " --> pdb=" O UNK M 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 400 through 404' Processing helix chain 'M' and resid 417 through 430 removed outlier: 4.125A pdb=" N ALA M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 448 Processing helix chain 'M' and resid 457 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.104A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 6.587A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.687A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.481A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 190 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 4.835A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.713A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.741A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.741A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.649A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.737A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.512A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.945A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.517A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.649A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 785 " --> pdb=" O MET C 768 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 722 through 727 removed outlier: 5.024A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.807A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.857A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.715A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 829 through 841 removed outlier: 6.830A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 865 through 866 Processing sheet with id=AD1, first strand: chain 'C' and resid 888 through 889 removed outlier: 3.980A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.620A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD4, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.136A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 353 through 356 removed outlier: 5.870A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 526 through 528 removed outlier: 4.091A pdb=" N LEU D 527 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.285A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AD9, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.554A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE2, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE3, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 5.210A pdb=" N LEU D1175 " --> pdb=" O ILE D1190 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D1190 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1264 through 1266 974 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 13.83 Time building geometry restraints manager: 11.88 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: 9111 1.34 - 1.46: 3770 1.46 - 1.57: 15358 1.57 - 1.69: 199 1.69 - 1.81: 162 Bond restraints: 28600 Sorted by residual: bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.592 -0.258 2.34e-02 1.83e+03 1.21e+02 bond pdb=" O3' DG F -5 " pdb=" P DC F -4 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.50e-02 4.44e+03 8.44e+01 bond pdb=" O3' DG G 16 " pdb=" P DC G 17 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.50e-02 4.44e+03 8.26e+01 bond pdb=" O3' DT F 6 " pdb=" P DG F 7 " ideal model delta sigma weight residual 1.607 1.502 0.105 1.50e-02 4.44e+03 4.87e+01 bond pdb=" C VAL D 858 " pdb=" N PRO D 859 " ideal model delta sigma weight residual 1.334 1.468 -0.134 2.34e-02 1.83e+03 3.29e+01 ... (remaining 28595 not shown) Histogram of bond angle deviations from ideal: 88.77 - 98.80: 12 98.80 - 108.83: 2485 108.83 - 118.86: 21612 118.86 - 128.89: 15059 128.89 - 138.92: 181 Bond angle restraints: 39349 Sorted by residual: angle pdb=" C4' DG F -5 " pdb=" C3' DG F -5 " pdb=" O3' DG F -5 " ideal model delta sigma weight residual 110.00 133.15 -23.15 1.50e+00 4.44e-01 2.38e+02 angle pdb=" O3' DG G 16 " pdb=" C3' DG G 16 " pdb=" C2' DG G 16 " ideal model delta sigma weight residual 111.50 88.77 22.73 1.50e+00 4.44e-01 2.30e+02 angle pdb=" C5' DG F -5 " pdb=" C4' DG F -5 " pdb=" C3' DG F -5 " ideal model delta sigma weight residual 114.90 93.59 21.31 1.50e+00 4.44e-01 2.02e+02 angle pdb=" O5' DG F -5 " pdb=" C5' DG F -5 " pdb=" C4' DG F -5 " ideal model delta sigma weight residual 110.80 127.85 -17.05 1.50e+00 4.44e-01 1.29e+02 angle pdb=" O3' DC F -6 " pdb=" C3' DC F -6 " pdb=" C2' DC F -6 " ideal model delta sigma weight residual 111.50 126.31 -14.81 1.50e+00 4.44e-01 9.75e+01 ... (remaining 39344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 16483 35.52 - 71.05: 611 71.05 - 106.57: 19 106.57 - 142.09: 2 142.09 - 177.62: 7 Dihedral angle restraints: 17122 sinusoidal: 6793 harmonic: 10329 Sorted by residual: dihedral pdb=" CA ALA C1263 " pdb=" C ALA C1263 " pdb=" N GLN C1264 " pdb=" CA GLN C1264 " ideal model delta harmonic sigma weight residual -180.00 -139.47 -40.53 0 5.00e+00 4.00e-02 6.57e+01 dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 142.29 37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA LYS D 118 " pdb=" C LYS D 118 " pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta harmonic sigma weight residual 180.00 144.02 35.98 0 5.00e+00 4.00e-02 5.18e+01 ... (remaining 17119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 4654 0.157 - 0.314: 68 0.314 - 0.472: 6 0.472 - 0.629: 4 0.629 - 0.786: 2 Chirality restraints: 4734 Sorted by residual: chirality pdb=" C3' DG F -5 " pdb=" C4' DG F -5 " pdb=" O3' DG F -5 " pdb=" C2' DG F -5 " both_signs ideal model delta sigma weight residual False -2.66 -1.87 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" P DC G 17 " pdb=" OP1 DC G 17 " pdb=" OP2 DC G 17 " pdb=" O5' DC G 17 " both_signs ideal model delta sigma weight residual True 2.35 -1.65 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA ALA D 546 " pdb=" N ALA D 546 " pdb=" C ALA D 546 " pdb=" CB ALA D 546 " both_signs ideal model delta sigma weight residual False 2.48 1.86 0.63 2.00e-01 2.50e+01 9.85e+00 ... (remaining 4731 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 0 " 0.227 2.00e-02 2.50e+03 1.05e-01 2.50e+02 pdb=" N1 DC F 0 " -0.079 2.00e-02 2.50e+03 pdb=" C2 DC F 0 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC F 0 " -0.103 2.00e-02 2.50e+03 pdb=" N3 DC F 0 " 0.038 2.00e-02 2.50e+03 pdb=" C4 DC F 0 " 0.052 2.00e-02 2.50e+03 pdb=" N4 DC F 0 " 0.088 2.00e-02 2.50e+03 pdb=" C5 DC F 0 " -0.064 2.00e-02 2.50e+03 pdb=" C6 DC F 0 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC F -4 " -0.132 2.00e-02 2.50e+03 6.44e-02 9.34e+01 pdb=" N1 DC F -4 " 0.104 2.00e-02 2.50e+03 pdb=" C2 DC F -4 " 0.038 2.00e-02 2.50e+03 pdb=" O2 DC F -4 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC F -4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC F -4 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC F -4 " -0.079 2.00e-02 2.50e+03 pdb=" C5 DC F -4 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DC F -4 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F -5 " -0.099 2.00e-02 2.50e+03 4.96e-02 7.38e+01 pdb=" N9 DG F -5 " 0.116 2.00e-02 2.50e+03 pdb=" C8 DG F -5 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DG F -5 " -0.032 2.00e-02 2.50e+03 pdb=" C5 DG F -5 " 0.036 2.00e-02 2.50e+03 pdb=" C6 DG F -5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG F -5 " -0.030 2.00e-02 2.50e+03 pdb=" N1 DG F -5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG F -5 " -0.028 2.00e-02 2.50e+03 pdb=" N2 DG F -5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG F -5 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG F -5 " 0.047 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 130 2.48 - 3.09: 19936 3.09 - 3.69: 39892 3.69 - 4.30: 55793 4.30 - 4.90: 90407 Nonbonded interactions: 206158 Sorted by model distance: nonbonded pdb=" N GLU D1327 " pdb=" OE1 GLU D1327 " model vdw 1.878 2.520 nonbonded pdb=" OE2 GLU A 165 " pdb=" N ARG A 166 " model vdw 2.022 2.520 nonbonded pdb=" O3' DG G -8 " pdb=" O4' DA G -7 " model vdw 2.067 3.040 nonbonded pdb=" C2' DT G -17 " pdb=" C7 DT G -16 " model vdw 2.194 3.860 nonbonded pdb=" O ILE D 937 " pdb=" N GLY D 939 " model vdw 2.197 2.520 ... (remaining 206153 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 5 through 57 or (resid 58 and (name N or name CA or name C \ or name O or name CB )) or resid 59 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 134 or (resid 135 through 136 and (name N or name CA o \ r name C or name O or name CB )) or resid 137 through 141 or (resid 142 and (nam \ e N or name CA or name C or name O or name CB )) or resid 143 through 157 or (re \ sid 158 through 160 and (name N or name CA or name C or name O or name CB )) or \ resid 161 through 162 or (resid 163 through 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 232 or (resid 233 \ and (name N or name CA or name C or name O or name CB )) or resid 234 or (resid \ 235 and (name N or name CA or name C or name O or name CB )) or resid 236 throug \ h 237)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 135 or (resid 136 and ( \ name N or name CA or name C or name O or name CB )) or resid 137 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ or (resid 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 216 or (resid 217 and (name N or name CA or name C or name O or \ name CB )) or resid 218 through 236 or (resid 237 and (name N or name CA or nam \ e C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.140 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 79.830 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.258 28600 Z= 0.293 Angle : 0.912 23.150 39349 Z= 0.542 Chirality : 0.059 0.786 4734 Planarity : 0.005 0.157 4806 Dihedral : 15.248 177.618 10448 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.29 % Favored : 90.12 % Rotamer: Outliers : 0.72 % Allowed : 1.57 % Favored : 97.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.11), residues: 3521 helix: -2.58 (0.12), residues: 1130 sheet: -1.31 (0.24), residues: 314 loop : -2.37 (0.11), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.004 0.000 HIS D 450 PHE 0.016 0.001 PHE D 620 TYR 0.020 0.001 TYR C1231 ARG 0.007 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 791 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.9132 (t0) cc_final: 0.8861 (m-30) REVERT: A 31 LEU cc_start: 0.8305 (mt) cc_final: 0.8077 (mt) REVERT: A 77 ASP cc_start: 0.8566 (m-30) cc_final: 0.8350 (m-30) REVERT: A 96 ASP cc_start: 0.6428 (p0) cc_final: 0.6029 (p0) REVERT: A 97 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7139 (pt0) REVERT: A 173 VAL cc_start: 0.8967 (m) cc_final: 0.8117 (p) REVERT: A 181 GLU cc_start: 0.9219 (tp30) cc_final: 0.8923 (mm-30) REVERT: A 215 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9164 (tp30) REVERT: B 46 ILE cc_start: 0.8828 (mt) cc_final: 0.8573 (mt) REVERT: B 96 ASP cc_start: 0.8723 (p0) cc_final: 0.8273 (m-30) REVERT: B 114 ASP cc_start: 0.9469 (m-30) cc_final: 0.9248 (p0) REVERT: B 118 ASP cc_start: 0.8744 (m-30) cc_final: 0.7957 (t70) REVERT: B 186 ASN cc_start: 0.8560 (t0) cc_final: 0.8125 (t0) REVERT: B 198 LEU cc_start: 0.8227 (mt) cc_final: 0.7801 (mp) REVERT: B 212 ASP cc_start: 0.8076 (t0) cc_final: 0.7628 (t0) REVERT: C 5 TYR cc_start: 0.8029 (t80) cc_final: 0.7583 (m-80) REVERT: C 23 ASP cc_start: 0.8974 (m-30) cc_final: 0.8675 (p0) REVERT: C 130 MET cc_start: 0.9309 (ttt) cc_final: 0.8749 (ttm) REVERT: C 195 PHE cc_start: 0.6892 (m-80) cc_final: 0.6416 (m-80) REVERT: C 419 ILE cc_start: 0.7940 (pt) cc_final: 0.7664 (pt) REVERT: C 469 VAL cc_start: 0.8854 (t) cc_final: 0.8630 (p) REVERT: C 473 ARG cc_start: 0.9105 (tpt90) cc_final: 0.8434 (tmm160) REVERT: C 526 HIS cc_start: 0.9074 (t70) cc_final: 0.8851 (t-90) REVERT: C 580 GLN cc_start: 0.8485 (pt0) cc_final: 0.7918 (pt0) REVERT: C 603 ILE cc_start: 0.9356 (pt) cc_final: 0.8830 (mp) REVERT: C 734 ILE cc_start: 0.9431 (mt) cc_final: 0.9120 (pt) REVERT: C 766 ASN cc_start: 0.8298 (t0) cc_final: 0.7723 (p0) REVERT: C 775 GLU cc_start: 0.9133 (tt0) cc_final: 0.8872 (pm20) REVERT: C 843 THR cc_start: 0.9623 (p) cc_final: 0.9331 (t) REVERT: C 857 VAL cc_start: 0.8707 (t) cc_final: 0.8401 (m) REVERT: C 946 LEU cc_start: 0.9158 (mp) cc_final: 0.8791 (pt) REVERT: C 974 ARG cc_start: 0.9474 (ttt90) cc_final: 0.9232 (ptp-170) REVERT: C 1019 ASP cc_start: 0.9622 (m-30) cc_final: 0.9323 (p0) REVERT: C 1040 ASP cc_start: 0.8267 (m-30) cc_final: 0.7814 (t0) REVERT: C 1140 LYS cc_start: 0.9390 (mmtp) cc_final: 0.9183 (mtmm) REVERT: C 1210 ILE cc_start: 0.8750 (tt) cc_final: 0.8463 (pt) REVERT: D 34 SER cc_start: 0.8099 (m) cc_final: 0.7866 (p) REVERT: D 60 ARG cc_start: 0.7862 (ttp-170) cc_final: 0.7488 (mtm110) REVERT: D 88 CYS cc_start: 0.8181 (m) cc_final: 0.7960 (m) REVERT: D 105 ILE cc_start: 0.9377 (tp) cc_final: 0.9095 (mt) REVERT: D 196 GLN cc_start: 0.9616 (mm-40) cc_final: 0.9371 (tm-30) REVERT: D 303 VAL cc_start: 0.9118 (t) cc_final: 0.8721 (p) REVERT: D 306 LEU cc_start: 0.8524 (tt) cc_final: 0.8107 (tp) REVERT: D 330 MET cc_start: 0.8116 (ttt) cc_final: 0.7851 (ttt) REVERT: D 339 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8102 (mtt180) REVERT: D 414 GLU cc_start: 0.9017 (tt0) cc_final: 0.8703 (tm-30) REVERT: D 437 PHE cc_start: 0.8599 (m-10) cc_final: 0.8050 (m-10) REVERT: D 442 ILE cc_start: 0.8760 (tp) cc_final: 0.8489 (tp) REVERT: D 591 ILE cc_start: 0.8262 (tp) cc_final: 0.7967 (pt) REVERT: D 809 VAL cc_start: 0.7634 (t) cc_final: 0.7344 (p) REVERT: D 810 THR cc_start: 0.8829 (t) cc_final: 0.8601 (p) REVERT: D 820 ILE cc_start: 0.8821 (mt) cc_final: 0.8489 (tt) REVERT: D 832 LYS cc_start: 0.7308 (mmmt) cc_final: 0.7046 (mmmt) REVERT: D 835 LEU cc_start: 0.8497 (tp) cc_final: 0.8222 (tt) REVERT: D 1146 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8789 (mt-10) REVERT: D 1149 ARG cc_start: 0.9317 (mtt180) cc_final: 0.8865 (mtm180) REVERT: D 1320 ILE cc_start: 0.9002 (mt) cc_final: 0.8720 (tp) REVERT: D 1328 THR cc_start: 0.8865 (p) cc_final: 0.8629 (m) REVERT: D 1357 ILE cc_start: 0.9128 (mt) cc_final: 0.8550 (pt) REVERT: E 5 THR cc_start: 0.8242 (m) cc_final: 0.7054 (p) REVERT: E 21 LEU cc_start: 0.8471 (mp) cc_final: 0.8264 (mt) REVERT: E 67 ARG cc_start: 0.8757 (mmt90) cc_final: 0.8548 (mmm160) REVERT: M 127 GLN cc_start: 0.9214 (tp40) cc_final: 0.8964 (tt0) REVERT: M 205 GLN cc_start: 0.8965 (pt0) cc_final: 0.8595 (pm20) REVERT: M 221 SER cc_start: 0.9071 (t) cc_final: 0.8848 (p) outliers start: 18 outliers final: 9 residues processed: 806 average time/residue: 0.4540 time to fit residues: 549.5768 Evaluate side-chains 430 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 421 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 934 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 5.9990 chunk 278 optimal weight: 30.0000 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 287 optimal weight: 30.0000 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 333 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS C 510 GLN C 526 HIS C 832 HIS C1061 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN D 861 ASN D 897 HIS D1218 HIS M 157 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28600 Z= 0.355 Angle : 0.775 12.026 39349 Z= 0.407 Chirality : 0.048 0.291 4734 Planarity : 0.005 0.074 4806 Dihedral : 18.500 179.125 4998 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.27 % Favored : 92.13 % Rotamer: Outliers : 3.34 % Allowed : 10.87 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.12 % 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: -2.10 (0.13), residues: 3521 helix: -0.32 (0.14), residues: 1175 sheet: -0.88 (0.26), residues: 332 loop : -2.24 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 409 HIS 0.008 0.002 HIS A 160 PHE 0.030 0.002 PHE D 629 TYR 0.027 0.002 TYR C1281 ARG 0.022 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 412 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8937 (t0) cc_final: 0.8687 (t70) REVERT: A 77 ASP cc_start: 0.8769 (m-30) cc_final: 0.8552 (m-30) REVERT: A 215 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9229 (tp30) REVERT: B 57 THR cc_start: 0.6465 (t) cc_final: 0.6255 (m) REVERT: B 131 CYS cc_start: 0.8775 (p) cc_final: 0.8521 (m) REVERT: B 210 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.6407 (p) REVERT: C 84 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8774 (pt0) REVERT: C 223 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9363 (pp) REVERT: C 336 LEU cc_start: 0.8234 (tp) cc_final: 0.7866 (pp) REVERT: C 407 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8955 (ttp80) REVERT: C 473 ARG cc_start: 0.9084 (tpt90) cc_final: 0.8395 (tmm160) REVERT: C 653 MET cc_start: 0.8995 (tpp) cc_final: 0.8763 (ttt) REVERT: C 674 ASP cc_start: 0.9183 (m-30) cc_final: 0.8654 (m-30) REVERT: C 843 THR cc_start: 0.9685 (p) cc_final: 0.9383 (t) REVERT: C 859 GLU cc_start: 0.8854 (mp0) cc_final: 0.8599 (pp20) REVERT: C 890 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7953 (pttt) REVERT: C 915 ASP cc_start: 0.8297 (m-30) cc_final: 0.7696 (t0) REVERT: C 1016 GLU cc_start: 0.9744 (mt-10) cc_final: 0.9485 (pp20) REVERT: C 1040 ASP cc_start: 0.8448 (m-30) cc_final: 0.8171 (t0) REVERT: C 1210 ILE cc_start: 0.8904 (tt) cc_final: 0.8664 (pt) REVERT: C 1304 MET cc_start: 0.9404 (tpp) cc_final: 0.8824 (tpp) REVERT: C 1321 GLU cc_start: 0.8811 (tp30) cc_final: 0.8538 (tp30) REVERT: D 60 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7694 (mtm110) REVERT: D 88 CYS cc_start: 0.8105 (m) cc_final: 0.7808 (m) REVERT: D 117 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7307 (tt) REVERT: D 206 ASN cc_start: 0.9531 (t0) cc_final: 0.9256 (m110) REVERT: D 248 ASP cc_start: 0.9034 (m-30) cc_final: 0.8606 (m-30) REVERT: D 306 LEU cc_start: 0.8823 (tt) cc_final: 0.8478 (tp) REVERT: D 330 MET cc_start: 0.8519 (ttt) cc_final: 0.8317 (ttp) REVERT: D 338 PHE cc_start: 0.8120 (m-80) cc_final: 0.7776 (m-10) REVERT: D 339 ARG cc_start: 0.8512 (mmt180) cc_final: 0.8154 (mtt180) REVERT: D 442 ILE cc_start: 0.9069 (tp) cc_final: 0.8532 (pt) REVERT: D 602 SER cc_start: 0.8833 (m) cc_final: 0.8529 (p) REVERT: D 719 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7900 (t80) REVERT: D 806 ASP cc_start: 0.8584 (t0) cc_final: 0.8258 (t0) REVERT: D 810 THR cc_start: 0.8876 (t) cc_final: 0.8639 (p) REVERT: D 820 ILE cc_start: 0.8649 (mt) cc_final: 0.8121 (tt) REVERT: D 825 VAL cc_start: 0.8686 (m) cc_final: 0.8218 (p) REVERT: D 830 ASP cc_start: 0.8508 (t0) cc_final: 0.7789 (t0) REVERT: D 832 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7460 (mmmt) REVERT: D 1040 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7290 (tpt) REVERT: D 1146 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8991 (mt-10) REVERT: D 1320 ILE cc_start: 0.9301 (mt) cc_final: 0.9009 (tp) REVERT: D 1357 ILE cc_start: 0.9423 (mt) cc_final: 0.8776 (pt) REVERT: E 5 THR cc_start: 0.8474 (m) cc_final: 0.7401 (p) REVERT: M 127 GLN cc_start: 0.9268 (tp40) cc_final: 0.9051 (tt0) REVERT: M 181 ARG cc_start: 0.8737 (ttt180) cc_final: 0.8098 (ttt180) REVERT: M 205 GLN cc_start: 0.8978 (pt0) cc_final: 0.8646 (pm20) outliers start: 83 outliers final: 40 residues processed: 467 average time/residue: 0.3977 time to fit residues: 293.3094 Evaluate side-chains 367 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 322 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 719 PHE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 277 optimal weight: 50.0000 chunk 226 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 chunk 297 optimal weight: 0.0470 chunk 331 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D 861 ASN M 157 GLN M 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28600 Z= 0.349 Angle : 0.730 11.477 39349 Z= 0.384 Chirality : 0.046 0.237 4734 Planarity : 0.005 0.094 4806 Dihedral : 18.367 178.396 4981 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 3.70 % Allowed : 13.76 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -1.57 (0.13), residues: 3521 helix: 0.51 (0.15), residues: 1193 sheet: -0.46 (0.27), residues: 322 loop : -2.24 (0.12), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 236 HIS 0.006 0.002 HIS D 651 PHE 0.024 0.002 PHE D 620 TYR 0.025 0.002 TYR D 537 ARG 0.009 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 338 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8806 (t0) cc_final: 0.8555 (t70) REVERT: B 29 GLU cc_start: 0.9345 (tt0) cc_final: 0.8928 (tm-30) REVERT: B 49 SER cc_start: 0.8650 (t) cc_final: 0.8282 (m) REVERT: B 210 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.6485 (p) REVERT: B 212 ASP cc_start: 0.7996 (t0) cc_final: 0.7543 (t0) REVERT: C 39 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 84 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8814 (mt-10) REVERT: C 223 LEU cc_start: 0.9538 (tt) cc_final: 0.9330 (pp) REVERT: C 225 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.6993 (t80) REVERT: C 336 LEU cc_start: 0.8486 (tp) cc_final: 0.7938 (pp) REVERT: C 370 MET cc_start: 0.8947 (tmm) cc_final: 0.8659 (tmm) REVERT: C 407 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8898 (ttp80) REVERT: C 473 ARG cc_start: 0.9123 (tpt90) cc_final: 0.8460 (tmm160) REVERT: C 653 MET cc_start: 0.9061 (tpp) cc_final: 0.8742 (ttt) REVERT: C 843 THR cc_start: 0.9695 (p) cc_final: 0.9480 (t) REVERT: C 890 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7977 (pttt) REVERT: C 915 ASP cc_start: 0.8572 (m-30) cc_final: 0.7997 (t0) REVERT: C 1040 ASP cc_start: 0.8630 (m-30) cc_final: 0.8332 (t0) REVERT: C 1321 GLU cc_start: 0.8885 (tp30) cc_final: 0.8571 (tp30) REVERT: D 60 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.8045 (mtm110) REVERT: D 206 ASN cc_start: 0.9539 (t0) cc_final: 0.9335 (m110) REVERT: D 306 LEU cc_start: 0.9019 (tt) cc_final: 0.8738 (tp) REVERT: D 332 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5356 (mmtt) REVERT: D 338 PHE cc_start: 0.8069 (m-80) cc_final: 0.7736 (m-10) REVERT: D 339 ARG cc_start: 0.8502 (mmt180) cc_final: 0.8089 (mtt180) REVERT: D 442 ILE cc_start: 0.8993 (tp) cc_final: 0.8410 (pt) REVERT: D 454 CYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8467 (m) REVERT: D 537 TYR cc_start: 0.8638 (t80) cc_final: 0.8389 (t80) REVERT: D 552 ILE cc_start: 0.9282 (mt) cc_final: 0.8827 (pt) REVERT: D 603 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8244 (tttm) REVERT: D 810 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8987 (p) REVERT: D 820 ILE cc_start: 0.8659 (mt) cc_final: 0.8079 (tt) REVERT: D 825 VAL cc_start: 0.8934 (m) cc_final: 0.8687 (p) REVERT: D 830 ASP cc_start: 0.8531 (t0) cc_final: 0.8085 (t0) REVERT: D 1040 MET cc_start: 0.8127 (ttt) cc_final: 0.7236 (tpt) REVERT: D 1357 ILE cc_start: 0.9293 (mt) cc_final: 0.9032 (pt) REVERT: E 18 ASP cc_start: 0.9164 (m-30) cc_final: 0.8951 (m-30) REVERT: M 181 ARG cc_start: 0.8553 (ttt180) cc_final: 0.8192 (ttt180) outliers start: 92 outliers final: 54 residues processed: 408 average time/residue: 0.3700 time to fit residues: 245.6045 Evaluate side-chains 359 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 36 optimal weight: 40.0000 chunk 159 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 354 optimal weight: 40.0000 chunk 175 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1244 GLN M 127 GLN M 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28600 Z= 0.224 Angle : 0.648 10.985 39349 Z= 0.337 Chirality : 0.043 0.269 4734 Planarity : 0.004 0.085 4806 Dihedral : 18.223 177.095 4979 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.04 % Favored : 91.34 % Rotamer: Outliers : 3.18 % Allowed : 15.81 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -1.26 (0.14), residues: 3521 helix: 0.93 (0.15), residues: 1201 sheet: -0.33 (0.28), residues: 327 loop : -2.17 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.005 0.001 HIS D 651 PHE 0.013 0.001 PHE D 620 TYR 0.021 0.002 TYR D 537 ARG 0.007 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 311 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9332 (tt0) cc_final: 0.8904 (tm-30) REVERT: B 49 SER cc_start: 0.8629 (t) cc_final: 0.8254 (m) REVERT: B 210 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.6497 (p) REVERT: B 212 ASP cc_start: 0.8024 (t0) cc_final: 0.7557 (t0) REVERT: C 84 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8812 (mt-10) REVERT: C 164 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6683 (p) REVERT: C 223 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9322 (pp) REVERT: C 336 LEU cc_start: 0.8534 (tp) cc_final: 0.8129 (pp) REVERT: C 407 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8923 (ttp80) REVERT: C 473 ARG cc_start: 0.9059 (tpt90) cc_final: 0.8514 (ttp80) REVERT: C 653 MET cc_start: 0.9046 (tpp) cc_final: 0.8696 (ttt) REVERT: C 758 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8288 (ttm170) REVERT: C 890 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7941 (pttt) REVERT: C 915 ASP cc_start: 0.8618 (m-30) cc_final: 0.8044 (t0) REVERT: C 964 LEU cc_start: 0.8314 (tp) cc_final: 0.8042 (mm) REVERT: C 974 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8714 (ptp-110) REVERT: C 1040 ASP cc_start: 0.8697 (m-30) cc_final: 0.8392 (t0) REVERT: C 1321 GLU cc_start: 0.8914 (tp30) cc_final: 0.8596 (tp30) REVERT: D 49 PHE cc_start: 0.8540 (m-80) cc_final: 0.8324 (m-80) REVERT: D 60 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7975 (mtm110) REVERT: D 306 LEU cc_start: 0.8907 (tt) cc_final: 0.8618 (tp) REVERT: D 308 ASP cc_start: 0.7435 (t0) cc_final: 0.7150 (t70) REVERT: D 338 PHE cc_start: 0.8089 (m-80) cc_final: 0.7808 (m-10) REVERT: D 339 ARG cc_start: 0.8453 (mmt180) cc_final: 0.8021 (mtt180) REVERT: D 442 ILE cc_start: 0.9025 (tp) cc_final: 0.8446 (pt) REVERT: D 454 CYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8323 (m) REVERT: D 537 TYR cc_start: 0.8840 (t80) cc_final: 0.8534 (t80) REVERT: D 544 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6953 (pp) REVERT: D 552 ILE cc_start: 0.9274 (mt) cc_final: 0.8840 (pt) REVERT: D 603 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8212 (tttt) REVERT: D 762 ASN cc_start: 0.8974 (m-40) cc_final: 0.8725 (m-40) REVERT: D 820 ILE cc_start: 0.8597 (mt) cc_final: 0.7999 (tt) REVERT: D 825 VAL cc_start: 0.8903 (m) cc_final: 0.8621 (p) REVERT: D 1040 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7291 (tpt) REVERT: D 1357 ILE cc_start: 0.9296 (mt) cc_final: 0.8819 (pt) REVERT: E 6 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7237 (t) REVERT: M 160 ASP cc_start: 0.9499 (m-30) cc_final: 0.9235 (p0) REVERT: M 295 PRO cc_start: 0.5431 (Cg_endo) cc_final: 0.5214 (Cg_exo) outliers start: 79 outliers final: 53 residues processed: 372 average time/residue: 0.3662 time to fit residues: 223.5945 Evaluate side-chains 341 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 280 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 0.0010 chunk 201 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 146 optimal weight: 40.0000 chunk 302 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 147 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D 929 GLN D1244 GLN M 157 GLN ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28600 Z= 0.227 Angle : 0.636 10.275 39349 Z= 0.331 Chirality : 0.042 0.221 4734 Planarity : 0.004 0.082 4806 Dihedral : 18.122 179.569 4979 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.97 % Favored : 90.51 % Rotamer: Outliers : 4.63 % Allowed : 15.53 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -1.08 (0.14), residues: 3521 helix: 1.13 (0.15), residues: 1211 sheet: -0.22 (0.28), residues: 321 loop : -2.12 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.004 0.001 HIS C 554 PHE 0.013 0.001 PHE D 620 TYR 0.024 0.001 TYR A 185 ARG 0.008 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 302 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9346 (tt0) cc_final: 0.8919 (tm-30) REVERT: B 49 SER cc_start: 0.8620 (t) cc_final: 0.8265 (m) REVERT: B 210 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.6451 (p) REVERT: C 39 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8496 (mt) REVERT: C 160 ASP cc_start: 0.8725 (p0) cc_final: 0.8491 (p0) REVERT: C 164 THR cc_start: 0.7010 (OUTLIER) cc_final: 0.6704 (p) REVERT: C 246 LEU cc_start: 0.9699 (tp) cc_final: 0.9455 (pp) REVERT: C 336 LEU cc_start: 0.8553 (tp) cc_final: 0.8107 (pp) REVERT: C 407 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8898 (ttp-110) REVERT: C 473 ARG cc_start: 0.9027 (tpt90) cc_final: 0.8456 (ttp80) REVERT: C 653 MET cc_start: 0.9019 (tpp) cc_final: 0.8703 (ttt) REVERT: C 678 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7442 (mmt90) REVERT: C 758 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8266 (ttm170) REVERT: C 915 ASP cc_start: 0.8625 (m-30) cc_final: 0.7984 (t0) REVERT: C 964 LEU cc_start: 0.8373 (tp) cc_final: 0.8057 (mm) REVERT: C 1040 ASP cc_start: 0.8732 (m-30) cc_final: 0.8453 (t0) REVERT: C 1321 GLU cc_start: 0.8930 (tp30) cc_final: 0.8610 (tp30) REVERT: D 60 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7993 (mtm110) REVERT: D 186 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.9222 (tm-30) REVERT: D 306 LEU cc_start: 0.8894 (tt) cc_final: 0.8620 (tp) REVERT: D 308 ASP cc_start: 0.7389 (t0) cc_final: 0.7121 (t70) REVERT: D 332 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5758 (mmtt) REVERT: D 339 ARG cc_start: 0.8312 (mmt180) cc_final: 0.7926 (mtt90) REVERT: D 410 ASP cc_start: 0.9256 (m-30) cc_final: 0.8964 (t0) REVERT: D 442 ILE cc_start: 0.9053 (tp) cc_final: 0.8472 (pt) REVERT: D 537 TYR cc_start: 0.8981 (t80) cc_final: 0.8647 (t80) REVERT: D 552 ILE cc_start: 0.9252 (mt) cc_final: 0.8771 (pt) REVERT: D 603 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8196 (tmtt) REVERT: D 762 ASN cc_start: 0.8974 (m-40) cc_final: 0.8696 (m-40) REVERT: D 820 ILE cc_start: 0.8585 (mt) cc_final: 0.7962 (tt) REVERT: D 825 VAL cc_start: 0.8921 (m) cc_final: 0.8650 (p) REVERT: D 1040 MET cc_start: 0.8079 (ttt) cc_final: 0.7221 (tpt) REVERT: D 1155 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8810 (tp) REVERT: D 1357 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8846 (pt) REVERT: E 67 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8434 (mmm-85) REVERT: M 160 ASP cc_start: 0.9500 (m-30) cc_final: 0.9231 (p0) outliers start: 115 outliers final: 71 residues processed: 392 average time/residue: 0.3712 time to fit residues: 239.0041 Evaluate side-chains 364 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 284 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 5.9990 chunk 319 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 208 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28600 Z= 0.214 Angle : 0.630 10.053 39349 Z= 0.327 Chirality : 0.042 0.264 4734 Planarity : 0.004 0.083 4806 Dihedral : 17.963 179.318 4979 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.69 % Favored : 90.77 % Rotamer: Outliers : 4.10 % Allowed : 16.30 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.94 (0.14), residues: 3521 helix: 1.30 (0.15), residues: 1218 sheet: -0.14 (0.28), residues: 320 loop : -2.09 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 183 HIS 0.004 0.001 HIS C 554 PHE 0.012 0.001 PHE D 620 TYR 0.024 0.001 TYR M 123 ARG 0.010 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 287 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9353 (tt0) cc_final: 0.8928 (tm-30) REVERT: B 49 SER cc_start: 0.8597 (t) cc_final: 0.8236 (m) REVERT: B 210 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.6551 (p) REVERT: C 160 ASP cc_start: 0.8720 (p0) cc_final: 0.8493 (p0) REVERT: C 164 THR cc_start: 0.7002 (OUTLIER) cc_final: 0.6690 (p) REVERT: C 246 LEU cc_start: 0.9697 (tp) cc_final: 0.9453 (pp) REVERT: C 407 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8896 (ttp-110) REVERT: C 473 ARG cc_start: 0.9039 (tpt90) cc_final: 0.8423 (ttp80) REVERT: C 678 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7493 (mmt90) REVERT: C 758 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8255 (ttm170) REVERT: C 915 ASP cc_start: 0.8730 (m-30) cc_final: 0.8052 (t0) REVERT: C 964 LEU cc_start: 0.8372 (tp) cc_final: 0.8038 (mm) REVERT: C 974 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8843 (ptp-110) REVERT: C 1040 ASP cc_start: 0.8726 (m-30) cc_final: 0.8382 (t0) REVERT: C 1321 GLU cc_start: 0.8931 (tp30) cc_final: 0.8609 (tp30) REVERT: D 60 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7955 (mtm110) REVERT: D 186 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.9230 (tm-30) REVERT: D 306 LEU cc_start: 0.8834 (tt) cc_final: 0.8567 (tp) REVERT: D 308 ASP cc_start: 0.7383 (t0) cc_final: 0.7116 (t70) REVERT: D 339 ARG cc_start: 0.8305 (mmt180) cc_final: 0.7945 (mtt180) REVERT: D 410 ASP cc_start: 0.9260 (m-30) cc_final: 0.8965 (t0) REVERT: D 442 ILE cc_start: 0.9068 (tp) cc_final: 0.8499 (pt) REVERT: D 552 ILE cc_start: 0.9247 (mt) cc_final: 0.8768 (pt) REVERT: D 603 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8298 (tmtt) REVERT: D 762 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8675 (m-40) REVERT: D 820 ILE cc_start: 0.8512 (mt) cc_final: 0.8070 (tt) REVERT: D 821 MET cc_start: 0.9013 (tpp) cc_final: 0.8747 (tpp) REVERT: D 825 VAL cc_start: 0.8928 (m) cc_final: 0.8667 (p) REVERT: D 1040 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7292 (tpt) REVERT: D 1146 GLU cc_start: 0.9437 (mm-30) cc_final: 0.8840 (mt-10) REVERT: D 1155 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8792 (tp) REVERT: D 1244 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: D 1357 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8868 (pt) REVERT: E 12 LYS cc_start: 0.8042 (tppp) cc_final: 0.7600 (tppp) REVERT: E 67 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8380 (mmm160) REVERT: M 160 ASP cc_start: 0.9499 (m-30) cc_final: 0.9215 (p0) REVERT: M 181 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8100 (ptm160) outliers start: 102 outliers final: 74 residues processed: 369 average time/residue: 0.3786 time to fit residues: 228.5134 Evaluate side-chains 366 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 282 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 353 optimal weight: 40.0000 chunk 221 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 163 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN D1244 GLN E 43 ASN M 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28600 Z= 0.271 Angle : 0.657 14.864 39349 Z= 0.339 Chirality : 0.043 0.243 4734 Planarity : 0.004 0.082 4806 Dihedral : 17.855 179.044 4979 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.34 % Favored : 90.06 % Rotamer: Outliers : 4.19 % Allowed : 16.34 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.94 (0.14), residues: 3521 helix: 1.39 (0.15), residues: 1202 sheet: -0.04 (0.28), residues: 333 loop : -2.16 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 183 HIS 0.004 0.001 HIS C 554 PHE 0.017 0.001 PHE D 338 TYR 0.019 0.002 TYR M 123 ARG 0.006 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 292 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9372 (tt0) cc_final: 0.8956 (tm-30) REVERT: B 49 SER cc_start: 0.8689 (t) cc_final: 0.8335 (m) REVERT: B 210 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.6656 (p) REVERT: C 39 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8619 (mt) REVERT: C 160 ASP cc_start: 0.8656 (p0) cc_final: 0.8412 (p0) REVERT: C 164 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6718 (p) REVERT: C 246 LEU cc_start: 0.9693 (tp) cc_final: 0.9448 (pp) REVERT: C 407 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8902 (ttp-110) REVERT: C 473 ARG cc_start: 0.9038 (tpt90) cc_final: 0.8572 (ttp80) REVERT: C 475 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8094 (p) REVERT: C 678 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7530 (mmt90) REVERT: C 758 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8282 (ttm170) REVERT: C 915 ASP cc_start: 0.8764 (m-30) cc_final: 0.8091 (t0) REVERT: C 964 LEU cc_start: 0.8352 (tp) cc_final: 0.8007 (mm) REVERT: C 1040 ASP cc_start: 0.8747 (m-30) cc_final: 0.8414 (t0) REVERT: C 1321 GLU cc_start: 0.8941 (tp30) cc_final: 0.8619 (tp30) REVERT: D 49 PHE cc_start: 0.8589 (m-80) cc_final: 0.8285 (m-80) REVERT: D 186 GLN cc_start: 0.9550 (OUTLIER) cc_final: 0.9245 (tm-30) REVERT: D 259 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.5014 (mpp-170) REVERT: D 306 LEU cc_start: 0.8901 (tt) cc_final: 0.8633 (tp) REVERT: D 308 ASP cc_start: 0.7617 (t0) cc_final: 0.7388 (t70) REVERT: D 339 ARG cc_start: 0.8335 (mmt180) cc_final: 0.8023 (mtm180) REVERT: D 410 ASP cc_start: 0.9234 (m-30) cc_final: 0.8951 (t0) REVERT: D 442 ILE cc_start: 0.9077 (tp) cc_final: 0.8503 (pt) REVERT: D 552 ILE cc_start: 0.9269 (mt) cc_final: 0.8788 (pt) REVERT: D 603 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8318 (tmtt) REVERT: D 666 GLU cc_start: 0.9620 (tp30) cc_final: 0.9396 (mm-30) REVERT: D 762 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8598 (m-40) REVERT: D 820 ILE cc_start: 0.8505 (mt) cc_final: 0.8054 (tt) REVERT: D 821 MET cc_start: 0.9028 (tpp) cc_final: 0.8775 (tpp) REVERT: D 825 VAL cc_start: 0.8987 (m) cc_final: 0.8729 (p) REVERT: D 1040 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7215 (tpt) REVERT: D 1155 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8873 (tp) REVERT: D 1357 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8932 (pt) REVERT: E 11 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8654 (mm-30) REVERT: E 64 LEU cc_start: 0.8829 (mt) cc_final: 0.8625 (mm) REVERT: E 67 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8393 (mmm160) REVERT: M 160 ASP cc_start: 0.9495 (m-30) cc_final: 0.9210 (p0) REVERT: M 181 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8017 (ptm160) outliers start: 104 outliers final: 76 residues processed: 371 average time/residue: 0.3860 time to fit residues: 230.9956 Evaluate side-chains 365 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 277 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 309 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 69 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 278 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28600 Z= 0.237 Angle : 0.642 13.833 39349 Z= 0.332 Chirality : 0.043 0.222 4734 Planarity : 0.004 0.081 4806 Dihedral : 17.694 179.072 4979 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.86 % Favored : 90.54 % Rotamer: Outliers : 3.66 % Allowed : 16.86 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.93 (0.14), residues: 3521 helix: 1.36 (0.15), residues: 1222 sheet: 0.02 (0.28), residues: 333 loop : -2.17 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 183 HIS 0.004 0.001 HIS C 554 PHE 0.014 0.001 PHE D 338 TYR 0.018 0.001 TYR A 185 ARG 0.012 0.000 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 286 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9366 (tt0) cc_final: 0.8944 (tm-30) REVERT: B 49 SER cc_start: 0.8686 (t) cc_final: 0.8338 (m) REVERT: B 210 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.6752 (p) REVERT: C 39 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8631 (mt) REVERT: C 160 ASP cc_start: 0.8629 (p0) cc_final: 0.8399 (p0) REVERT: C 164 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6789 (p) REVERT: C 213 LEU cc_start: 0.9140 (mp) cc_final: 0.8901 (mp) REVERT: C 246 LEU cc_start: 0.9717 (tp) cc_final: 0.9485 (pp) REVERT: C 407 ARG cc_start: 0.9143 (tpp80) cc_final: 0.8901 (ttp-110) REVERT: C 473 ARG cc_start: 0.9033 (tpt90) cc_final: 0.8572 (ttp80) REVERT: C 475 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 678 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7521 (mmt90) REVERT: C 758 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8268 (ttm170) REVERT: C 915 ASP cc_start: 0.8745 (m-30) cc_final: 0.8054 (t0) REVERT: C 964 LEU cc_start: 0.8319 (tp) cc_final: 0.7972 (mm) REVERT: C 974 ARG cc_start: 0.9226 (ttm110) cc_final: 0.8782 (ptp-110) REVERT: C 1040 ASP cc_start: 0.8815 (m-30) cc_final: 0.8518 (t0) REVERT: C 1321 GLU cc_start: 0.8934 (tp30) cc_final: 0.8615 (tp30) REVERT: D 49 PHE cc_start: 0.8598 (m-80) cc_final: 0.8290 (m-80) REVERT: D 186 GLN cc_start: 0.9548 (OUTLIER) cc_final: 0.9246 (tm-30) REVERT: D 259 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5045 (mpp-170) REVERT: D 306 LEU cc_start: 0.8877 (tt) cc_final: 0.8603 (tp) REVERT: D 339 ARG cc_start: 0.8319 (mmt180) cc_final: 0.8014 (mtm180) REVERT: D 410 ASP cc_start: 0.9231 (m-30) cc_final: 0.8947 (t0) REVERT: D 442 ILE cc_start: 0.9097 (tp) cc_final: 0.8531 (pt) REVERT: D 552 ILE cc_start: 0.9265 (mt) cc_final: 0.8792 (pt) REVERT: D 666 GLU cc_start: 0.9619 (tp30) cc_final: 0.9399 (mm-30) REVERT: D 762 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8628 (m-40) REVERT: D 820 ILE cc_start: 0.8498 (mt) cc_final: 0.8059 (tt) REVERT: D 821 MET cc_start: 0.9064 (tpp) cc_final: 0.8819 (tpp) REVERT: D 825 VAL cc_start: 0.9010 (m) cc_final: 0.8774 (p) REVERT: D 993 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 1040 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7172 (tpt) REVERT: D 1146 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8804 (mt-10) REVERT: D 1155 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8905 (tp) REVERT: D 1357 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8954 (pt) REVERT: E 64 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8608 (mm) REVERT: E 67 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8409 (mmm160) REVERT: M 160 ASP cc_start: 0.9516 (m-30) cc_final: 0.9242 (p0) REVERT: M 181 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8085 (ttt180) outliers start: 91 outliers final: 70 residues processed: 355 average time/residue: 0.3839 time to fit residues: 221.3540 Evaluate side-chains 361 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 278 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1297 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 309 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 chunk 311 optimal weight: 0.4980 chunk 328 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN M 157 GLN M 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28600 Z= 0.327 Angle : 0.691 13.522 39349 Z= 0.356 Chirality : 0.044 0.286 4734 Planarity : 0.005 0.082 4806 Dihedral : 17.620 178.410 4979 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.83 % Favored : 89.58 % Rotamer: Outliers : 4.06 % Allowed : 16.74 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.98 (0.14), residues: 3521 helix: 1.31 (0.15), residues: 1223 sheet: 0.23 (0.29), residues: 320 loop : -2.23 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 115 HIS 0.005 0.001 HIS D 419 PHE 0.021 0.001 PHE D 338 TYR 0.022 0.002 TYR A 185 ARG 0.011 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 290 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.9382 (tt0) cc_final: 0.8988 (tm-30) REVERT: B 49 SER cc_start: 0.8704 (t) cc_final: 0.8353 (m) REVERT: B 210 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.6896 (p) REVERT: C 39 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8718 (mt) REVERT: C 84 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8697 (mt-10) REVERT: C 164 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6728 (p) REVERT: C 246 LEU cc_start: 0.9723 (tp) cc_final: 0.9497 (pp) REVERT: C 407 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8898 (ttp-110) REVERT: C 473 ARG cc_start: 0.9043 (tpt90) cc_final: 0.8600 (ttp80) REVERT: C 475 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8045 (p) REVERT: C 678 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7560 (mmt90) REVERT: C 915 ASP cc_start: 0.8782 (m-30) cc_final: 0.8138 (t0) REVERT: C 964 LEU cc_start: 0.8345 (tp) cc_final: 0.7977 (mm) REVERT: C 974 ARG cc_start: 0.9279 (ttm110) cc_final: 0.8859 (ptp-110) REVERT: C 1040 ASP cc_start: 0.8867 (m-30) cc_final: 0.8542 (t0) REVERT: C 1321 GLU cc_start: 0.8955 (tp30) cc_final: 0.8729 (tp30) REVERT: D 49 PHE cc_start: 0.8485 (m-80) cc_final: 0.8172 (m-80) REVERT: D 186 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9226 (tm-30) REVERT: D 259 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5114 (mpp-170) REVERT: D 306 LEU cc_start: 0.8947 (tt) cc_final: 0.8723 (tp) REVERT: D 339 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8054 (mtm180) REVERT: D 410 ASP cc_start: 0.9235 (m-30) cc_final: 0.8957 (t0) REVERT: D 442 ILE cc_start: 0.9102 (tp) cc_final: 0.8523 (pt) REVERT: D 666 GLU cc_start: 0.9612 (tp30) cc_final: 0.9401 (mm-30) REVERT: D 762 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8639 (m-40) REVERT: D 820 ILE cc_start: 0.8509 (mt) cc_final: 0.8072 (tt) REVERT: D 825 VAL cc_start: 0.9017 (m) cc_final: 0.8808 (p) REVERT: D 993 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8171 (mt-10) REVERT: D 1040 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7087 (tpt) REVERT: D 1155 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.8966 (tp) REVERT: D 1357 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9015 (pt) REVERT: E 64 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8612 (mm) REVERT: E 67 ARG cc_start: 0.8661 (tpp80) cc_final: 0.8385 (mmm160) REVERT: M 181 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8049 (ttt180) outliers start: 101 outliers final: 78 residues processed: 365 average time/residue: 0.3778 time to fit residues: 224.9530 Evaluate side-chains 374 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 284 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 137 ASP Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 309 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 0.9990 chunk 348 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 365 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 GLN M 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28600 Z= 0.175 Angle : 0.641 13.646 39349 Z= 0.328 Chirality : 0.042 0.275 4734 Planarity : 0.004 0.079 4806 Dihedral : 17.468 179.327 4979 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.49 % Favored : 90.88 % Rotamer: Outliers : 2.66 % Allowed : 18.35 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.83 (0.14), residues: 3521 helix: 1.43 (0.15), residues: 1225 sheet: 0.29 (0.29), residues: 320 loop : -2.13 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 115 HIS 0.003 0.001 HIS C 554 PHE 0.010 0.001 PHE D 620 TYR 0.024 0.001 TYR A 185 ARG 0.010 0.000 ARG C 974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7042 Ramachandran restraints generated. 3521 Oldfield, 0 Emsley, 3521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 294 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8888 (tpt90) REVERT: B 29 GLU cc_start: 0.9356 (tt0) cc_final: 0.8925 (tm-30) REVERT: B 49 SER cc_start: 0.8556 (t) cc_final: 0.8206 (m) REVERT: B 147 GLN cc_start: 0.8126 (pt0) cc_final: 0.7838 (pm20) REVERT: B 210 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.6816 (p) REVERT: C 39 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8489 (mt) REVERT: C 164 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6785 (p) REVERT: C 246 LEU cc_start: 0.9729 (tp) cc_final: 0.9495 (pp) REVERT: C 407 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8865 (ttp-110) REVERT: C 473 ARG cc_start: 0.9026 (tpt90) cc_final: 0.8437 (ttp80) REVERT: C 678 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7498 (mmt90) REVERT: C 915 ASP cc_start: 0.8738 (m-30) cc_final: 0.8078 (t0) REVERT: C 964 LEU cc_start: 0.8293 (tp) cc_final: 0.7930 (mm) REVERT: C 974 ARG cc_start: 0.9283 (ttm110) cc_final: 0.8858 (ptp-110) REVERT: C 1040 ASP cc_start: 0.8832 (m-30) cc_final: 0.8536 (t0) REVERT: C 1321 GLU cc_start: 0.8908 (tp30) cc_final: 0.8584 (tp30) REVERT: D 49 PHE cc_start: 0.8469 (m-80) cc_final: 0.8158 (m-80) REVERT: D 186 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9259 (tm-30) REVERT: D 259 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5184 (mpp-170) REVERT: D 306 LEU cc_start: 0.8824 (tt) cc_final: 0.8562 (tp) REVERT: D 339 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7947 (mtm180) REVERT: D 410 ASP cc_start: 0.9240 (m-30) cc_final: 0.8963 (t0) REVERT: D 442 ILE cc_start: 0.9109 (tp) cc_final: 0.8555 (pt) REVERT: D 762 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8628 (m-40) REVERT: D 821 MET cc_start: 0.9082 (tpp) cc_final: 0.8725 (tpp) REVERT: D 1040 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6899 (tpt) REVERT: D 1155 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.8886 (tp) REVERT: D 1357 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8978 (pt) REVERT: E 11 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8428 (mm-30) REVERT: E 67 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8393 (mmm160) REVERT: M 181 ARG cc_start: 0.8419 (ttt180) cc_final: 0.8077 (ttt180) outliers start: 66 outliers final: 50 residues processed: 342 average time/residue: 0.4037 time to fit residues: 222.6207 Evaluate side-chains 339 residues out of total 3027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 278 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 395 TYR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 678 ARG Chi-restraints excluded: chain C residue 740 GLU Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 762 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 157 GLN Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 309 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 268 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 36 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN M 157 GLN M 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094401 restraints weight = 53953.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092031 restraints weight = 41384.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092124 restraints weight = 37781.580| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28600 Z= 0.212 Angle : 0.648 13.428 39349 Z= 0.331 Chirality : 0.042 0.272 4734 Planarity : 0.004 0.079 4806 Dihedral : 17.406 178.241 4979 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.29 % Favored : 90.12 % Rotamer: Outliers : 2.74 % Allowed : 18.59 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.03 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -0.81 (0.14), residues: 3521 helix: 1.46 (0.15), residues: 1226 sheet: 0.12 (0.28), residues: 349 loop : -2.12 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 115 HIS 0.004 0.001 HIS C 554 PHE 0.012 0.001 PHE D 338 TYR 0.024 0.001 TYR A 185 ARG 0.010 0.000 ARG C 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5942.45 seconds wall clock time: 107 minutes 59.04 seconds (6479.04 seconds total)