Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:43:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/04_2023/6uan_20708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/04_2023/6uan_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_20708/04_2023/6uan_20708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/04_2023/6uan_20708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/04_2023/6uan_20708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uan_20708/04_2023/6uan_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 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.35, per 1000 atoms: 0.57 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 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: 0.63 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: 1.72 Time building geometry restraints manager: 3.14 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 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: 0.340 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: 0.000 Extract box with map and model: 2.460 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 7.56 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 : 0.980 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: 0.2274 time to fit residues: 63.2754 Evaluate side-chains 157 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0702 time to fit residues: 1.3952 ------------------------------------------------------------------------------- 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: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 A 225 ASN 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2075 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 : 0.610 6.733 10616 Z= 0.318 Chirality : 0.041 0.134 1218 Planarity : 0.004 0.041 1358 Dihedral : 5.904 58.566 1089 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 3.48 % 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: -4.14 (0.21), residues: 987 helix: -2.66 (0.17), residues: 526 sheet: -3.44 (0.61), residues: 47 loop : -2.59 (0.27), residues: 414 *********************** 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 226 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 0.929 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: 27 outliers final: 14 residues processed: 214 average time/residue: 0.1939 time to fit residues: 55.7888 Evaluate side-chains 178 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0941 time to fit residues: 3.4333 ------------------------------------------------------------------------------- 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: 0.1980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 ** Z 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7828 Z= 0.156 Angle : 0.581 7.467 10616 Z= 0.295 Chirality : 0.041 0.180 1218 Planarity : 0.003 0.037 1358 Dihedral : 5.356 56.598 1089 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 1.55 % 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: -3.16 (0.24), residues: 987 helix: -1.72 (0.20), residues: 526 sheet: -2.84 (0.68), residues: 47 loop : -2.38 (0.28), residues: 414 *********************** 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 218 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 0.965 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: 12 outliers final: 6 residues processed: 212 average time/residue: 0.1955 time to fit residues: 55.6906 Evaluate side-chains 178 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0753 time to fit residues: 2.0671 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 636 GLN ** 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: 0.7917 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7828 Z= 0.154 Angle : 0.586 8.132 10616 Z= 0.298 Chirality : 0.040 0.139 1218 Planarity : 0.003 0.033 1358 Dihedral : 5.057 55.252 1089 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.45 % 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: -2.62 (0.25), residues: 987 helix: -1.14 (0.21), residues: 522 sheet: -2.57 (0.76), residues: 41 loop : -2.36 (0.28), residues: 424 *********************** 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 218 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 211 average time/residue: 0.1923 time to fit residues: 55.1162 Evaluate side-chains 184 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0694 time to fit residues: 2.5005 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 9 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: 0.7919 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7828 Z= 0.160 Angle : 0.591 8.198 10616 Z= 0.301 Chirality : 0.041 0.151 1218 Planarity : 0.003 0.033 1358 Dihedral : 4.930 53.592 1089 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -2.35 (0.25), residues: 987 helix: -1.02 (0.21), residues: 525 sheet: -2.20 (0.77), residues: 41 loop : -2.11 (0.29), residues: 421 *********************** 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 208 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 200 average time/residue: 0.1869 time to fit residues: 51.2897 Evaluate side-chains 176 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1128 time to fit residues: 2.4196 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 636 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: 0.7985 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7828 Z= 0.245 Angle : 0.622 8.785 10616 Z= 0.318 Chirality : 0.042 0.143 1218 Planarity : 0.004 0.033 1358 Dihedral : 5.096 53.905 1089 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 3.22 % 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: -2.26 (0.25), residues: 987 helix: -0.96 (0.21), residues: 523 sheet: -2.27 (0.73), residues: 47 loop : -2.01 (0.29), residues: 417 *********************** 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 197 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 0.1848 time to fit residues: 46.7492 Evaluate side-chains 172 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0752 time to fit residues: 3.1478 ------------------------------------------------------------------------------- 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: 2.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7828 Z= 0.159 Angle : 0.608 9.269 10616 Z= 0.303 Chirality : 0.041 0.163 1218 Planarity : 0.003 0.031 1358 Dihedral : 4.776 48.810 1089 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.80 % 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: -2.01 (0.26), residues: 987 helix: -0.67 (0.22), residues: 514 sheet: -2.04 (0.70), residues: 47 loop : -2.02 (0.29), residues: 426 *********************** 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 200 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 194 average time/residue: 0.1966 time to fit residues: 51.9712 Evaluate side-chains 172 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0812 time to fit residues: 1.8881 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 65 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3790 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= 0.169 Angle : 0.637 9.093 10616 Z= 0.315 Chirality : 0.042 0.165 1218 Planarity : 0.003 0.031 1358 Dihedral : 4.740 47.344 1089 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.55 % 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: -1.93 (0.26), residues: 987 helix: -0.61 (0.22), residues: 513 sheet: -1.97 (0.70), residues: 53 loop : -1.98 (0.29), residues: 421 *********************** 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 193 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 188 average time/residue: 0.1960 time to fit residues: 49.9360 Evaluate side-chains 170 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1615 time to fit residues: 2.1640 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7828 Z= 0.165 Angle : 0.642 10.312 10616 Z= 0.319 Chirality : 0.042 0.191 1218 Planarity : 0.005 0.120 1358 Dihedral : 4.653 45.139 1089 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.64 % 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: -1.82 (0.26), residues: 987 helix: -0.52 (0.22), residues: 514 sheet: -1.78 (0.72), residues: 47 loop : -1.94 (0.29), residues: 426 *********************** 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 183 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 181 average time/residue: 0.1785 time to fit residues: 44.7381 Evaluate side-chains 167 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0724 time to fit residues: 1.5637 ------------------------------------------------------------------------------- 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: 1.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 7828 Z= 0.181 Angle : 0.690 13.974 10616 Z= 0.339 Chirality : 0.043 0.190 1218 Planarity : 0.004 0.045 1358 Dihedral : 4.616 43.850 1089 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -1.82 (0.26), residues: 987 helix: -0.54 (0.22), residues: 517 sheet: -1.64 (0.73), residues: 47 loop : -1.95 (0.29), residues: 423 ********************** 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 175 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 173 average time/residue: 0.1716 time to fit residues: 41.8720 Evaluate side-chains 167 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3340 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095920 restraints weight = 18189.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098290 restraints weight = 11832.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099903 restraints weight = 8928.446| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4216 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= 0.189 Angle : 0.687 10.926 10616 Z= 0.342 Chirality : 0.043 0.203 1218 Planarity : 0.003 0.030 1358 Dihedral : 4.617 42.364 1089 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -1.75 (0.26), residues: 987 helix: -0.46 (0.22), residues: 516 sheet: -1.64 (0.74), residues: 47 loop : -1.95 (0.29), residues: 424 =============================================================================== Job complete usr+sys time: 1791.60 seconds wall clock time: 33 minutes 3.94 seconds (1983.94 seconds total)