Starting phenix.real_space_refine (version: dev) on Sun Dec 11 21:39:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/12_2022/6uan_20708_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "Z GLU 41": "OE1" <-> "OE2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "Z GLU 71": "OE1" <-> "OE2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "Z GLU 155": "OE1" <-> "OE2" Residue "Z PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C ASP 576": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1847 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 225} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1746 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 224} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2022 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 247} Chain breaks: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2070 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 Time building chain proxies: 5.08, per 1000 atoms: 0.66 Number of scatterers: 7685 At special positions: 0 Unit cell: (94.34, 98.58, 106, 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 32 16.00 P 2 15.00 O 1449 8.00 N 1318 7.00 C 4884 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: 3.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 3 sheets defined 49.1% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.653A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.631A pdb=" N ALA A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 67 removed outlier: 3.764A pdb=" N ASN A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 removed outlier: 3.738A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 113 through 128 removed outlier: 3.601A pdb=" N TYR A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 158 removed outlier: 4.062A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.893A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 4.381A pdb=" N GLN A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.579A pdb=" N ASP A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 17 removed outlier: 3.859A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 7 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN Z 16 " --> pdb=" O LYS Z 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA Z 17 " --> pdb=" O LEU Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 32 removed outlier: 3.591A pdb=" N MET Z 27 " --> pdb=" O MET Z 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Z 28 " --> pdb=" O ALA Z 24 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU Z 29 " --> pdb=" O ALA Z 25 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL Z 30 " --> pdb=" O ALA Z 26 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR Z 31 " --> pdb=" O MET Z 27 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU Z 32 " --> pdb=" O LYS Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 68 removed outlier: 4.146A pdb=" N SER Z 46 " --> pdb=" O ARG Z 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG Z 56 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER Z 59 " --> pdb=" O ALA Z 55 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL Z 62 " --> pdb=" O SER Z 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER Z 65 " --> pdb=" O ARG Z 61 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN Z 68 " --> pdb=" O SER Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 104 removed outlier: 3.718A pdb=" N TYR Z 83 " --> pdb=" O MET Z 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL Z 85 " --> pdb=" O LYS Z 81 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS Z 86 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL Z 87 " --> pdb=" O TYR Z 83 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU Z 93 " --> pdb=" O LYS Z 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Z 94 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS Z 95 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP Z 97 " --> pdb=" O GLU Z 93 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS Z 104 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 109 No H-bonds generated for 'chain 'Z' and resid 106 through 109' Processing helix chain 'Z' and resid 116 through 133 removed outlier: 3.785A pdb=" N LEU Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY Z 124 " --> pdb=" O LEU Z 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR Z 126 " --> pdb=" O MET Z 122 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR Z 127 " --> pdb=" O LYS Z 123 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL Z 133 " --> pdb=" O TYR Z 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 154 removed outlier: 3.972A pdb=" N VAL Z 143 " --> pdb=" O ASN Z 140 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU Z 144 " --> pdb=" O SER Z 141 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN Z 147 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS Z 148 " --> pdb=" O ASP Z 145 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN Z 151 " --> pdb=" O LYS Z 148 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP Z 152 " --> pdb=" O ALA Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 181 removed outlier: 3.549A pdb=" N ALA Z 172 " --> pdb=" O ARG Z 168 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR Z 179 " --> pdb=" O PHE Z 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR Z 180 " --> pdb=" O SER Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 201 removed outlier: 3.675A pdb=" N ALA Z 193 " --> pdb=" O ALA Z 189 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP Z 199 " --> pdb=" O GLN Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 213 through 230 removed outlier: 3.834A pdb=" N LEU Z 217 " --> pdb=" O LYS Z 213 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE Z 218 " --> pdb=" O ASP Z 214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG Z 223 " --> pdb=" O MET Z 219 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR Z 227 " --> pdb=" O ARG Z 223 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU Z 228 " --> pdb=" O ASP Z 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 removed outlier: 4.473A pdb=" N LYS B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 550 through 553 No H-bonds generated for 'chain 'B' and resid 550 through 553' Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.615A pdb=" N ALA B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 639 through 651 removed outlier: 4.319A pdb=" N ILE B 644 " --> pdb=" O TYR B 640 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 708 through 718 removed outlier: 3.502A pdb=" N ALA B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 714 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 504 removed outlier: 3.634A pdb=" N GLN C 496 " --> pdb=" O PRO C 492 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY C 503 " --> pdb=" O LYS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 554 through 559 removed outlier: 3.627A pdb=" N GLN C 559 " --> pdb=" O ASP C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 569 Processing helix chain 'C' and resid 622 through 626 Processing helix chain 'C' and resid 639 through 650 Processing helix chain 'C' and resid 663 through 668 removed outlier: 4.166A pdb=" N PHE C 667 " --> pdb=" O ASP C 663 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 663 through 668' Processing helix chain 'C' and resid 687 through 696 removed outlier: 4.205A pdb=" N MET C 693 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 694 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 695 " --> pdb=" O ARG C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 716 removed outlier: 4.012A pdb=" N ILE C 714 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 716 " --> pdb=" O ALA C 712 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 470 through 472 Processing sheet with id= B, first strand: chain 'C' and resid 516 through 520 removed outlier: 6.457A pdb=" N VAL C 528 " --> pdb=" O MET C 517 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR C 519 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 526 " --> pdb=" O TYR C 519 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 529 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 481 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 482 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 470 " --> pdb=" O MET C 484 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 464 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS C 473 " --> pdb=" O ARG C 462 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 462 " --> pdb=" O LYS C 473 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.880A pdb=" N SER C 535 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2244 1.33 - 1.45: 1202 1.45 - 1.57: 4321 1.57 - 1.69: 8 1.69 - 1.81: 53 Bond restraints: 7828 Sorted by residual: bond pdb=" N SER C 720 " pdb=" CA SER C 720 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.01e+00 bond pdb=" C ILE A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.17e+00 bond pdb=" C LYS C 522 " pdb=" N PRO C 523 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.59e+00 bond pdb=" C LYS B 522 " pdb=" N PRO B 523 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.43e+00 bond pdb=" CA SEP B 729 " pdb=" C SEP B 729 " ideal model delta sigma weight residual 1.525 1.488 0.037 2.10e-02 2.27e+03 3.14e+00 ... (remaining 7823 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.92: 150 105.92 - 113.08: 4273 113.08 - 120.23: 3157 120.23 - 127.38: 2961 127.38 - 134.53: 75 Bond angle restraints: 10616 Sorted by residual: angle pdb=" C HIS B 574 " pdb=" N ARG B 575 " pdb=" CA ARG B 575 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C HIS C 585 " pdb=" N GLU C 586 " pdb=" CA GLU C 586 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" CG1 ILE C 582 " pdb=" CB ILE C 582 " pdb=" CG2 ILE C 582 " ideal model delta sigma weight residual 110.70 101.20 9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CA LEU B 525 " pdb=" CB LEU B 525 " pdb=" CG LEU B 525 " ideal model delta sigma weight residual 116.30 126.54 -10.24 3.50e+00 8.16e-02 8.56e+00 angle pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 120.83 122.60 -1.77 6.10e-01 2.69e+00 8.45e+00 ... (remaining 10611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4140 17.14 - 34.28: 462 34.28 - 51.41: 111 51.41 - 68.55: 16 68.55 - 85.69: 14 Dihedral angle restraints: 4743 sinusoidal: 1786 harmonic: 2957 Sorted by residual: dihedral pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N ALA A 159 " pdb=" CA ALA A 159 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA VAL Z 35 " pdb=" C VAL Z 35 " pdb=" N GLU Z 36 " pdb=" CA GLU Z 36 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASP B 555 " pdb=" C ASP B 555 " pdb=" N ILE B 556 " pdb=" CA ILE B 556 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 4740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 857 0.054 - 0.109: 299 0.109 - 0.163: 51 0.163 - 0.218: 10 0.218 - 0.272: 1 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CB VAL C 590 " pdb=" CA VAL C 590 " pdb=" CG1 VAL C 590 " pdb=" CG2 VAL C 590 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 724 " pdb=" CA ILE B 724 " pdb=" CG1 ILE B 724 " pdb=" CG2 ILE B 724 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 457 " pdb=" CA ILE C 457 " pdb=" CG1 ILE C 457 " pdb=" CG2 ILE C 457 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1215 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 491 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO C 492 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 492 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 492 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 707 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO C 708 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 708 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 708 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 721 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 722 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 722 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 722 " 0.028 5.00e-02 4.00e+02 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2037 2.78 - 3.31: 7250 3.31 - 3.84: 12297 3.84 - 4.37: 14088 4.37 - 4.90: 22995 Nonbonded interactions: 58667 Sorted by model distance: nonbonded pdb=" O PHE Z 154 " pdb=" OG SER Z 157 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR C 651 " pdb=" O LYS C 680 " model vdw 2.273 2.440 nonbonded pdb=" OG SER Z 38 " pdb=" OE1 GLU Z 41 " model vdw 2.277 2.440 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 176 " model vdw 2.286 2.440 nonbonded pdb=" O ASN A 112 " pdb=" OG SER A 115 " model vdw 2.293 2.440 ... (remaining 58662 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 3 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 through 17 or (resid 18 and (name \ N or name CA or name C or name O or name CB )) or resid 19 through 39 or (resid \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or res \ id 70 through 73 or (resid 74 through 76 and (name N or name CA or name C or nam \ e O or name CB )) or resid 77 or (resid 78 through 80 and (name N or name CA or \ name C or name O or name CB )) or resid 81 through 92 or (resid 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 103 or (resid 10 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 105 through 113 or (resid 114 and (name N or name CA or name C or name \ O or name CB )) or resid 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB )) or resid 123 through 143 or (resid 144 and \ (name N or name CA or name C or name O or name CB )) or resid 145 through 160 or \ (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 2 through 180 or (resid 181 and (name N or name CA or name C or name O or name C \ B )) or resid 182 through 194 or (resid 195 through 196 and (name N or name CA o \ r name C or name O or name CB )) or resid 197 through 202 or (resid 203 through \ 206 and (name N or name CA or name C or name O or name CB )) or resid 207 throug \ h 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 or (resid 213 through 214 and (name N or name CA or name C \ or name O or name CB )) or resid 215 through 219 or (resid 220 and (name N or n \ ame CA or name C or name O or name CB )) or resid 221 through 232)) selection = (chain 'Z' and (resid 3 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 232)) } ncs_group { reference = (chain 'B' and (resid 449 through 485 or (resid 486 through 487 and (name N or n \ ame CA or name C or name O or name CB )) or resid 488 through 521 or (resid 522 \ and (name N or name CA or name C or name O or name CB )) or resid 523 through 54 \ 6 or (resid 547 and (name N or name CA or name C or name O or name CB )) or resi \ d 548 through 625 or (resid 626 through 631 and (name N or name CA or name C or \ name O or name CB )) or resid 632 through 647 or (resid 648 and (name N or name \ CA or name C or name O or name CB )) or resid 649 through 677 or (resid 678 thro \ ugh 685 and (name N or name CA or name C or name O or name CB )) or resid 686 or \ (resid 687 through 691 and (name N or name CA or name C or name O or name CB )) \ or resid 692 or (resid 693 through 695 and (name N or name CA or name C or name \ O or name CB )) or resid 696 through 698 or (resid 699 through 703 and (name N \ or name CA or name C or name O or name CB )) or resid 704 through 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 723 or (resid 724 through 725 and (name N or name CA or name C or name O or na \ me CB )) or resid 726 through 729 or (resid 730 and (name N or name CA or name C \ or name O or name CB )) or resid 731 through 733)) selection = (chain 'C' and (resid 449 through 600 or resid 622 through 628 or resid 631 thro \ ugh 649 or (resid 650 and (name N or name CA or name C or name O or name CB or n \ ame CG or name SD )) or resid 651 through 657 or resid 676 through 682 or (resid \ 683 through 685 and (name N or name CA or name C or name O or name CB )) or res \ id 686 through 733)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 4884 2.51 5 N 1318 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.490 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.007 0.055 7828 Z= 0.476 Angle : 0.946 10.241 10616 Z= 0.503 Chirality : 0.056 0.272 1218 Planarity : 0.006 0.076 1358 Dihedral : 16.091 85.692 2827 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.19), residues: 987 helix: -4.03 (0.12), residues: 495 sheet: -3.95 (0.58), residues: 42 loop : -2.81 (0.25), residues: 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 0.966 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 outliers start: 8 outliers final: 1 residues processed: 215 average time/residue: 0.2139 time to fit residues: 59.9585 Evaluate side-chains 157 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0674 time to fit residues: 1.4656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 77 GLN A 140 ASN A 151 GLN A 165 HIS Z 9 GLN Z 140 ASN Z 147 GLN Z 151 GLN B 510 HIS B 581 ASN B 636 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 HIS C 530 GLN C 542 HIS C 562 GLN C 636 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7828 Z= 0.163 Angle : 0.612 7.246 10616 Z= 0.319 Chirality : 0.041 0.129 1218 Planarity : 0.004 0.040 1358 Dihedral : 5.818 58.297 1089 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.22), residues: 987 helix: -2.61 (0.17), residues: 525 sheet: -3.40 (0.61), residues: 47 loop : -2.56 (0.27), residues: 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 0.970 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 outliers start: 28 outliers final: 14 residues processed: 220 average time/residue: 0.1917 time to fit residues: 56.6719 Evaluate side-chains 185 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0939 time to fit residues: 3.4470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Z 9 GLN Z 151 GLN ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7828 Z= 0.163 Angle : 0.590 7.952 10616 Z= 0.300 Chirality : 0.041 0.129 1218 Planarity : 0.003 0.034 1358 Dihedral : 5.388 57.087 1089 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.24), residues: 987 helix: -1.70 (0.20), residues: 525 sheet: -2.91 (0.67), residues: 47 loop : -2.37 (0.28), residues: 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.025 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 outliers start: 15 outliers final: 8 residues processed: 204 average time/residue: 0.1765 time to fit residues: 49.7133 Evaluate side-chains 175 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0783 time to fit residues: 2.3889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Z 9 GLN Z 147 GLN B 581 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7828 Z= 0.154 Angle : 0.575 7.985 10616 Z= 0.292 Chirality : 0.040 0.141 1218 Planarity : 0.003 0.052 1358 Dihedral : 5.059 54.977 1089 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.25), residues: 987 helix: -1.10 (0.21), residues: 523 sheet: -2.68 (0.70), residues: 47 loop : -2.29 (0.28), residues: 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 208 average time/residue: 0.1762 time to fit residues: 51.2194 Evaluate side-chains 181 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0725 time to fit residues: 2.6194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 32 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 9 GLN Z 151 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7828 Z= 0.206 Angle : 0.597 7.889 10616 Z= 0.305 Chirality : 0.042 0.148 1218 Planarity : 0.003 0.030 1358 Dihedral : 5.101 54.621 1089 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.25), residues: 987 helix: -0.94 (0.21), residues: 529 sheet: -2.49 (0.72), residues: 47 loop : -2.08 (0.29), residues: 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 196 average time/residue: 0.1713 time to fit residues: 46.9266 Evaluate side-chains 168 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1023 time to fit residues: 2.9326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 0.0670 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7828 Z= 0.205 Angle : 0.620 10.166 10616 Z= 0.313 Chirality : 0.042 0.155 1218 Planarity : 0.004 0.034 1358 Dihedral : 5.050 52.331 1089 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.26), residues: 987 helix: -0.75 (0.22), residues: 524 sheet: -2.37 (0.73), residues: 47 loop : -2.02 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 184 average time/residue: 0.1720 time to fit residues: 44.8059 Evaluate side-chains 164 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0798 time to fit residues: 2.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 0.0020 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 494 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7828 Z= 0.153 Angle : 0.614 9.049 10616 Z= 0.304 Chirality : 0.042 0.163 1218 Planarity : 0.003 0.031 1358 Dihedral : 4.762 47.494 1089 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 987 helix: -0.52 (0.23), residues: 512 sheet: -2.09 (0.72), residues: 47 loop : -1.96 (0.29), residues: 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 189 average time/residue: 0.1656 time to fit residues: 44.4295 Evaluate side-chains 174 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0788 time to fit residues: 2.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7828 Z= 0.174 Angle : 0.614 9.973 10616 Z= 0.304 Chirality : 0.042 0.153 1218 Planarity : 0.003 0.031 1358 Dihedral : 4.742 47.429 1089 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.26), residues: 987 helix: -0.38 (0.23), residues: 512 sheet: -2.06 (0.71), residues: 53 loop : -1.91 (0.29), residues: 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 186 average time/residue: 0.1706 time to fit residues: 44.3687 Evaluate side-chains 164 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1640 time to fit residues: 1.9672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7828 Z= 0.162 Angle : 0.654 13.820 10616 Z= 0.322 Chirality : 0.042 0.204 1218 Planarity : 0.003 0.032 1358 Dihedral : 4.639 44.729 1089 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.26), residues: 987 helix: -0.36 (0.23), residues: 510 sheet: -1.94 (0.71), residues: 47 loop : -1.84 (0.29), residues: 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 175 average time/residue: 0.1522 time to fit residues: 38.5060 Evaluate side-chains 169 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0770 time to fit residues: 1.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.0040 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7828 Z= 0.170 Angle : 0.676 10.770 10616 Z= 0.334 Chirality : 0.043 0.218 1218 Planarity : 0.003 0.030 1358 Dihedral : 4.567 42.976 1089 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 987 helix: -0.26 (0.23), residues: 509 sheet: -1.77 (0.72), residues: 47 loop : -1.82 (0.30), residues: 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 178 average time/residue: 0.1524 time to fit residues: 39.4168 Evaluate side-chains 164 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1075 time to fit residues: 1.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0000 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096186 restraints weight = 18616.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098581 restraints weight = 11895.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100241 restraints weight = 8954.311| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 7828 Z= 0.172 Angle : 0.691 11.457 10616 Z= 0.339 Chirality : 0.042 0.217 1218 Planarity : 0.003 0.031 1358 Dihedral : 4.466 40.774 1089 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 987 helix: -0.24 (0.23), residues: 513 sheet: -1.42 (0.76), residues: 47 loop : -1.85 (0.29), residues: 427 =============================================================================== Job complete usr+sys time: 1765.62 seconds wall clock time: 32 minutes 32.39 seconds (1952.39 seconds total)