Starting phenix.real_space_refine on Fri Aug 22 20:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_20708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_20708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_20708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_20708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uan_20708/08_2025/6uan_20708.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 11, 'ARG:plan': 1, 'GLN:plan1': 3, '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, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} 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: {'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 132 Time building chain proxies: 2.16, per 1000 atoms: 0.28 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 - 3.00 Amino acid : True - 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: 0.62 Conformation dependent library (CDL) restraints added in 461.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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... Secondary structure from input PDB file: 41 helices and 5 sheets defined 55.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.616A pdb=" N GLU A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) 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 20 through 28 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) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 38 through 68 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 76 through 105 removed outlier: 3.837A pdb=" N ALA A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) 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 106 through 110 removed outlier: 3.513A pdb=" N LYS A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 129 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 138 through 159 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 165 through 182 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 185 through 202 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 208 through 231 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 4 through 18 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 19 through 31 removed outlier: 3.548A pdb=" N MET Z 23 " --> pdb=" O ARG Z 19 " (cutoff:3.500A) 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) Processing helix chain 'Z' and resid 41 through 69 removed outlier: 3.868A pdb=" N LEU Z 45 " --> pdb=" O GLU Z 41 " (cutoff:3.500A) 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 73 through 105 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 105 through 110 Processing helix chain 'Z' and resid 115 through 134 removed outlier: 3.688A pdb=" N TYR Z 119 " --> pdb=" O SER Z 115 " (cutoff:3.500A) 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 155 removed outlier: 3.987A pdb=" N ASN Z 140 " --> pdb=" O GLY Z 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL Z 142 " --> pdb=" O THR Z 138 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Z 144 " --> pdb=" O ASN Z 140 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP Z 145 " --> pdb=" O SER Z 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP Z 152 " --> pdb=" O LYS Z 148 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA Z 153 " --> pdb=" O ALA Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 182 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 188 through 202 removed outlier: 3.706A pdb=" N LEU Z 192 " --> pdb=" O LYS Z 188 " (cutoff:3.500A) 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) removed outlier: 3.611A pdb=" N ALA Z 202 " --> pdb=" O ASP Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 212 through 231 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 493 through 506 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 536 through 542 Processing helix chain 'B' and resid 549 through 554 removed outlier: 3.702A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.987A pdb=" N GLN B 559 " --> pdb=" O ASP B 555 " (cutoff:3.500A) 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 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.586A pdb=" N ASP B 587 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.537A pdb=" N SER B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 638 through 652 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 687 through 695 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.953A pdb=" N ARG B 704 " --> pdb=" O ARG B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 719 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) removed outlier: 3.887A pdb=" N ARG B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 505 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 543 Processing helix chain 'C' and resid 553 through 560 removed outlier: 3.505A pdb=" N ALA C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) 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 570 Processing helix chain 'C' and resid 621 through 627 Processing helix chain 'C' and resid 638 through 651 Processing helix chain 'C' and resid 664 through 669 removed outlier: 3.864A pdb=" N MET C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 697 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) removed outlier: 3.663A pdb=" N LEU C 697 " --> pdb=" O MET C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 715 removed outlier: 4.012A pdb=" N ILE C 714 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 462 through 466 removed outlier: 3.851A pdb=" N VAL B 471 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B 465 " --> pdb=" O GLY B 469 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 582 through 583 Processing sheet with id=AA3, first strand: chain 'C' and resid 462 through 465 removed outlier: 6.402A pdb=" N ARG C 462 " --> pdb=" O LYS C 473 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS C 473 " --> pdb=" O ARG C 462 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 464 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 470 " --> pdb=" O MET C 484 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 482 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 481 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 529 " --> pdb=" O ALA C 481 " (cutoff:3.500A) Processing sheet with id=AA4, 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) Processing sheet with id=AA5, first strand: chain 'C' and resid 572 through 573 304 hydrogen bonds defined for protein. 885 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: 1.09 Time building geometry restraints manager: 0.86 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: 0.00 - 2.05: 10170 2.05 - 4.10: 381 4.10 - 6.14: 40 6.14 - 8.19: 17 8.19 - 10.24: 8 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: 2021 2.78 - 3.31: 7213 3.31 - 3.84: 12231 3.84 - 4.37: 13985 4.37 - 4.90: 22973 Nonbonded interactions: 58423 Sorted by model distance: nonbonded pdb=" O PHE Z 154 " pdb=" OG SER Z 157 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR C 651 " pdb=" O LYS C 680 " model vdw 2.273 3.040 nonbonded pdb=" OG SER Z 38 " pdb=" OE1 GLU Z 41 " model vdw 2.277 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 176 " model vdw 2.286 3.040 nonbonded pdb=" O ASN A 112 " pdb=" OG SER A 115 " model vdw 2.293 3.040 ... (remaining 58418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.530 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- 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= 0.329 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 % Allowed : 14.18 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.033 0.003 TYR A 49 PHE 0.023 0.003 PHE B 595 TRP 0.012 0.002 TRP A 229 HIS 0.006 0.002 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00723 ( 7828) covalent geometry : angle 0.94631 (10616) hydrogen bonds : bond 0.31572 ( 304) hydrogen bonds : angle 10.31511 ( 885) *********************** 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 to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.306 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: Z 9 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7907 (tp-100) REVERT: Z 150 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 472 TYR cc_start: 0.7201 (m-10) cc_final: 0.6985 (m-80) REVERT: B 484 MET cc_start: 0.7983 (ptp) cc_final: 0.7779 (ptp) REVERT: B 506 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7646 (mtt-85) REVERT: B 548 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 565 ASP cc_start: 0.8255 (t70) cc_final: 0.7999 (t0) REVERT: B 581 ASN cc_start: 0.8311 (p0) cc_final: 0.8107 (p0) REVERT: B 691 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8507 (ttm-80) REVERT: B 703 GLU cc_start: 0.8800 (pp20) cc_final: 0.8316 (pp20) REVERT: C 575 ARG cc_start: 0.8255 (ttt180) cc_final: 0.8017 (ttt-90) REVERT: C 638 ASP cc_start: 0.9298 (t0) cc_final: 0.9002 (t0) REVERT: C 697 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (pp) outliers start: 8 outliers final: 1 residues processed: 215 average time/residue: 0.1068 time to fit residues: 29.9903 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 150 TYR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 697 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 140 ASN A 151 GLN A 165 HIS Z 9 GLN Z 140 ASN B 486 ASN B 510 HIS C 510 HIS C 530 GLN C 542 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093791 restraints weight = 18213.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096391 restraints weight = 11297.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098161 restraints weight = 8288.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.099369 restraints weight = 6760.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100045 restraints weight = 5886.614| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2236 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= 0.130 Angle : 0.655 10.270 10616 Z= 0.343 Chirality : 0.043 0.145 1218 Planarity : 0.004 0.039 1358 Dihedral : 6.283 56.678 1096 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.22 % Allowed : 18.43 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.15 (0.21), residues: 987 helix: -2.62 (0.16), residues: 541 sheet: -3.33 (0.65), residues: 42 loop : -2.70 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 575 TYR 0.031 0.002 TYR B 647 PHE 0.036 0.002 PHE A 154 TRP 0.011 0.001 TRP A 60 HIS 0.005 0.001 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7828) covalent geometry : angle 0.65491 (10616) hydrogen bonds : bond 0.05363 ( 304) hydrogen bonds : angle 5.61856 ( 885) *********************** 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 235 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8281 (pp20) cc_final: 0.7313 (pm20) REVERT: Z 9 GLN cc_start: 0.8567 (tp40) cc_final: 0.8241 (tp-100) REVERT: Z 150 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: B 484 MET cc_start: 0.8329 (ptp) cc_final: 0.8025 (ptt) REVERT: B 548 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: B 581 ASN cc_start: 0.8376 (p0) cc_final: 0.8132 (p0) REVERT: B 703 GLU cc_start: 0.8854 (pp20) cc_final: 0.8232 (pp20) REVERT: B 733 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5817 (tt) REVERT: C 462 ARG cc_start: 0.7791 (tmm-80) cc_final: 0.7445 (ttt-90) REVERT: C 501 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8505 (mm-30) REVERT: C 545 GLU cc_start: 0.7695 (mp0) cc_final: 0.7431 (mp0) REVERT: C 552 LYS cc_start: 0.8427 (pttt) cc_final: 0.7754 (pttm) REVERT: C 577 LEU cc_start: 0.9286 (tp) cc_final: 0.9043 (tt) REVERT: C 583 PHE cc_start: 0.8096 (t80) cc_final: 0.7718 (m-80) REVERT: C 697 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8607 (pp) outliers start: 25 outliers final: 9 residues processed: 223 average time/residue: 0.0823 time to fit residues: 25.6520 Evaluate side-chains 192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 150 TYR Chi-restraints excluded: chain Z residue 164 THR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 695 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 697 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Z 151 GLN C 540 HIS ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094516 restraints weight = 17900.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097044 restraints weight = 11015.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098835 restraints weight = 8039.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100044 restraints weight = 6485.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100882 restraints weight = 5617.067| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7828 Z= 0.118 Angle : 0.614 9.368 10616 Z= 0.315 Chirality : 0.042 0.139 1218 Planarity : 0.003 0.034 1358 Dihedral : 5.842 57.114 1096 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.22 % Allowed : 20.88 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.23), residues: 987 helix: -1.70 (0.19), residues: 535 sheet: -2.79 (0.73), residues: 42 loop : -2.40 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 575 TYR 0.013 0.001 TYR A 180 PHE 0.022 0.002 PHE Z 118 TRP 0.007 0.001 TRP A 229 HIS 0.007 0.001 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7828) covalent geometry : angle 0.61426 (10616) hydrogen bonds : bond 0.04473 ( 304) hydrogen bonds : angle 5.10470 ( 885) *********************** 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 234 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.322 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: A 116 LYS cc_start: 0.8667 (mttt) cc_final: 0.8166 (mttm) REVERT: A 119 TYR cc_start: 0.9074 (m-80) cc_final: 0.8715 (m-80) REVERT: A 154 PHE cc_start: 0.7065 (m-80) cc_final: 0.6596 (m-80) REVERT: Z 9 GLN cc_start: 0.8474 (tp40) cc_final: 0.8254 (tp-100) REVERT: B 517 MET cc_start: 0.7829 (mmm) cc_final: 0.7106 (mmt) REVERT: B 548 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: B 647 TYR cc_start: 0.8511 (t80) cc_final: 0.8157 (t80) REVERT: B 703 GLU cc_start: 0.8870 (pp20) cc_final: 0.8241 (pp20) REVERT: B 733 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.6021 (tt) REVERT: C 462 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.7596 (ttt-90) REVERT: C 506 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8050 (ttm110) REVERT: C 545 GLU cc_start: 0.7620 (mp0) cc_final: 0.7331 (mp0) REVERT: C 552 LYS cc_start: 0.8423 (pttt) cc_final: 0.7644 (pttm) REVERT: C 583 PHE cc_start: 0.7926 (t80) cc_final: 0.7649 (m-80) REVERT: C 697 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8636 (pp) outliers start: 25 outliers final: 11 residues processed: 224 average time/residue: 0.0770 time to fit residues: 24.4276 Evaluate side-chains 192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 164 THR Chi-restraints excluded: chain Z residue 175 PHE Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 697 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 151 GLN B 486 ASN B 542 HIS B 581 ASN B 709 GLN C 581 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093511 restraints weight = 18672.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096020 restraints weight = 11497.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097761 restraints weight = 8408.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098955 restraints weight = 6827.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099314 restraints weight = 5926.967| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3040 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= 0.124 Angle : 0.617 8.605 10616 Z= 0.315 Chirality : 0.042 0.149 1218 Planarity : 0.004 0.031 1358 Dihedral : 5.602 57.149 1094 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.87 % Allowed : 23.45 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.25), residues: 987 helix: -1.11 (0.21), residues: 529 sheet: -2.58 (0.76), residues: 42 loop : -2.13 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.017 0.001 TYR A 180 PHE 0.039 0.002 PHE Z 197 TRP 0.007 0.001 TRP A 229 HIS 0.004 0.001 HIS C 585 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7828) covalent geometry : angle 0.61745 (10616) hydrogen bonds : bond 0.04003 ( 304) hydrogen bonds : angle 4.88866 ( 885) *********************** 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 222 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.344 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: A 119 TYR cc_start: 0.9057 (m-80) cc_final: 0.8846 (m-80) REVERT: A 154 PHE cc_start: 0.7184 (m-80) cc_final: 0.6861 (m-80) REVERT: Z 150 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: Z 212 TYR cc_start: 0.7879 (p90) cc_final: 0.7464 (p90) REVERT: B 472 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: B 517 MET cc_start: 0.7845 (mmm) cc_final: 0.7158 (mmt) REVERT: B 548 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: B 647 TYR cc_start: 0.8592 (t80) cc_final: 0.8345 (t80) REVERT: B 648 GLU cc_start: 0.8325 (tp30) cc_final: 0.8083 (tp30) REVERT: B 696 CYS cc_start: 0.8975 (m) cc_final: 0.8553 (m) REVERT: B 711 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 733 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5763 (tt) REVERT: C 462 ARG cc_start: 0.7929 (tmm-80) cc_final: 0.7578 (ttt-90) REVERT: C 501 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 506 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8124 (ttm110) REVERT: C 545 GLU cc_start: 0.7720 (mp0) cc_final: 0.7439 (mp0) REVERT: C 552 LYS cc_start: 0.8381 (pttt) cc_final: 0.7585 (pttm) REVERT: C 583 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: C 697 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8645 (pp) outliers start: 30 outliers final: 18 residues processed: 210 average time/residue: 0.0807 time to fit residues: 23.6969 Evaluate side-chains 202 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain Z residue 8 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 150 TYR Chi-restraints excluded: chain Z residue 164 THR Chi-restraints excluded: chain Z residue 175 PHE Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 540 HIS Chi-restraints excluded: chain C residue 583 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 619 TRP Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 697 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9757 > 50: distance: 35 - 38: 33.850 distance: 38 - 39: 55.852 distance: 39 - 40: 40.680 distance: 39 - 42: 56.807 distance: 40 - 44: 41.184 distance: 42 - 43: 39.377 distance: 44 - 45: 38.826 distance: 45 - 46: 57.616 distance: 46 - 47: 28.107 distance: 46 - 52: 42.093 distance: 47 - 74: 38.655 distance: 48 - 49: 24.000 distance: 49 - 50: 59.076 distance: 49 - 51: 42.952 distance: 52 - 58: 40.808 distance: 54 - 55: 39.695 distance: 55 - 83: 42.011 distance: 56 - 57: 39.902 distance: 59 - 60: 22.625 distance: 60 - 61: 43.710 distance: 60 - 63: 16.183 distance: 61 - 62: 39.802 distance: 61 - 68: 6.241 distance: 62 - 90: 55.791 distance: 63 - 64: 39.334 distance: 64 - 65: 41.883 distance: 65 - 66: 51.400 distance: 65 - 67: 9.244 distance: 68 - 69: 41.336 distance: 69 - 70: 40.140 distance: 69 - 72: 40.316 distance: 70 - 71: 39.995 distance: 70 - 74: 56.531 distance: 71 - 101: 54.016 distance: 72 - 73: 39.623 distance: 74 - 75: 57.643 distance: 75 - 76: 43.928 distance: 75 - 78: 5.812 distance: 76 - 77: 46.536 distance: 76 - 83: 41.126 distance: 77 - 113: 38.027 distance: 78 - 79: 51.291 distance: 80 - 81: 39.521 distance: 83 - 84: 32.786 distance: 84 - 85: 32.561 distance: 84 - 87: 40.390 distance: 85 - 86: 6.811 distance: 85 - 90: 8.536 distance: 86 - 121: 35.911 distance: 87 - 88: 31.657 distance: 87 - 89: 52.471 distance: 90 - 91: 55.983 distance: 91 - 92: 55.913 distance: 91 - 94: 40.903 distance: 92 - 93: 40.933 distance: 93 - 128: 35.186 distance: 94 - 95: 40.527 distance: 95 - 96: 40.670 distance: 95 - 97: 31.658 distance: 96 - 98: 67.505 distance: 97 - 99: 32.921 distance: 98 - 100: 37.376 distance: 99 - 100: 33.042 distance: 101 - 102: 40.079 distance: 102 - 103: 10.345 distance: 102 - 105: 40.568 distance: 103 - 104: 8.217 distance: 103 - 113: 9.197 distance: 104 - 134: 36.600 distance: 106 - 107: 23.483 distance: 106 - 108: 18.201 distance: 107 - 109: 16.619 distance: 108 - 110: 18.227 distance: 109 - 111: 14.135 distance: 110 - 111: 14.236 distance: 111 - 112: 46.505 distance: 115 - 121: 35.069 distance: 116 - 140: 37.095 distance: 117 - 118: 14.678 distance: 118 - 119: 24.037 distance: 118 - 120: 24.428