Starting phenix.real_space_refine on Tue Sep 24 12:33:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ced_16606/09_2024/8ced_16606.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1340 5.49 5 S 71 5.16 5 C 27407 2.51 5 N 9534 2.21 5 O 13612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51964 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 28597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 28597 Classifications: {'RNA': 1333} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 81, 'rna3p_pur': 643, 'rna3p_pyr': 496} Link IDs: {'rna2p': 193, 'rna3p': 1139} Chain breaks: 3 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 5650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5650 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 27, 'TRANS': 680} Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "F" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1490 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "I" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 128} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "T" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "U" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 730 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1615 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 3, 'TRANS': 201} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "K" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "N" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Time building chain proxies: 21.19, per 1000 atoms: 0.41 Number of scatterers: 51964 At special positions: 0 Unit cell: (191.2, 224, 200, 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 71 16.00 P 1340 15.00 O 13612 8.00 N 9534 7.00 C 27407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.02 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: 8.78 Conformation dependent library (CDL) restraints added in 2.6 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5444 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 33 sheets defined 42.7% alpha, 21.8% beta 414 base pairs and 771 stacking pairs defined. Time for finding SS restraints: 19.31 Creating SS restraints... Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.621A pdb=" N LEU C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.833A pdb=" N LYS C 171 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.517A pdb=" N HIS C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 289 through 294 removed outlier: 4.197A pdb=" N TYR C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 392 through 413 Processing helix chain 'C' and resid 442 through 467 removed outlier: 3.503A pdb=" N ILE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 493 removed outlier: 3.666A pdb=" N THR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 514 removed outlier: 3.915A pdb=" N LEU C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 533 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 582 through 623 Proline residue: C 594 - end of helix Processing helix chain 'C' and resid 624 through 627 removed outlier: 3.885A pdb=" N ILE C 627 " --> pdb=" O LEU C 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 624 through 627' Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 24 through 29 removed outlier: 4.000A pdb=" N ARG D 29 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 63 removed outlier: 3.809A pdb=" N LYS D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 removed outlier: 4.612A pdb=" N ASP D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER D 79 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.734A pdb=" N ARG D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 131 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 169 through 178 Processing helix chain 'D' and resid 206 through 226 removed outlier: 3.625A pdb=" N ALA D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 16 Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.502A pdb=" N LYS F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 93 through 101 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 143 through 147 removed outlier: 4.266A pdb=" N ASN F 147 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.590A pdb=" N ILE F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 115 through 122 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 26 removed outlier: 3.736A pdb=" N LYS L 26 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.558A pdb=" N GLY L 131 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.638A pdb=" N THR O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 78 through 88 Processing helix chain 'S' and resid 5 through 41 removed outlier: 3.506A pdb=" N VAL S 35 " --> pdb=" O ALA S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.671A pdb=" N LYS S 56 " --> pdb=" O THR S 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA S 61 " --> pdb=" O ARG S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 85 Processing helix chain 'T' and resid 15 through 33 removed outlier: 3.529A pdb=" N ASN T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU T 30 " --> pdb=" O PHE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 82 removed outlier: 3.603A pdb=" N VAL T 72 " --> pdb=" O ASP T 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 30 through 35 Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 53 through 70 Processing helix chain 'V' and resid 61 through 80 removed outlier: 3.679A pdb=" N GLU V 78 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS V 79 " --> pdb=" O GLY V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 103 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.846A pdb=" N GLY E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 removed outlier: 3.533A pdb=" N GLY E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.529A pdb=" N GLU E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 144 removed outlier: 3.749A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.596A pdb=" N SER H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 Processing helix chain 'H' and resid 92 through 111 removed outlier: 3.524A pdb=" N THR H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 129 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 55 Proline residue: J 51 - end of helix Processing helix chain 'J' and resid 71 through 91 removed outlier: 3.938A pdb=" N GLU J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.703A pdb=" N ALA J 101 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.542A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.538A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.738A pdb=" N TYR M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.804A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 3.505A pdb=" N ASN M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'R' and resid 12 through 25 removed outlier: 3.534A pdb=" N LYS R 18 " --> pdb=" O HIS R 14 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR R 25 " --> pdb=" O LYS R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'R' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 98 removed outlier: 7.231A pdb=" N ILE C 111 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE C 132 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET C 113 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 139 through 146 removed outlier: 6.005A pdb=" N PHE C 165 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 198 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 196 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR C 185 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL C 198 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS C 183 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS C 179 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS C 178 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 249 through 251 removed outlier: 4.368A pdb=" N LYS C 364 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 355 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.014A pdb=" N THR C 258 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA7, first strand: chain 'C' and resid 422 through 427 removed outlier: 4.238A pdb=" N GLU C 422 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 630 through 638 removed outlier: 5.550A pdb=" N ILE C 635 " --> pdb=" O GLU C 646 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU C 646 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU C 652 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE C 705 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 654 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE C 707 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N HIS C 656 " --> pdb=" O ILE C 707 " (cutoff:3.500A) removed outlier: 12.750A pdb=" N GLY C 709 " --> pdb=" O HIS C 656 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C 703 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 696 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE C 705 " --> pdb=" O VAL C 694 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL C 694 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE C 707 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS C 692 " --> pdb=" O ILE C 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 665 through 668 Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 4.570A pdb=" N THR D 33 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 90 through 92 removed outlier: 6.026A pdb=" N LEU D 68 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE D 164 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL D 70 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AB5, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 25 removed outlier: 5.518A pdb=" N GLU G 13 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY G 40 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU G 15 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL G 38 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 28 " --> pdb=" O VAL G 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 85 through 89 Processing sheet with id=AB8, first strand: chain 'I' and resid 24 through 27 Processing sheet with id=AB9, first strand: chain 'I' and resid 76 through 79 Processing sheet with id=AC1, first strand: chain 'I' and resid 76 through 79 removed outlier: 5.239A pdb=" N VAL I 127 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER I 107 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA I 129 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 53 removed outlier: 5.494A pdb=" N CYS L 47 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG L 69 " --> pdb=" O CYS L 47 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG L 49 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR L 108 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU L 94 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLY L 113 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 11.796A pdb=" N VAL L 92 " --> pdb=" O GLY L 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.560A pdb=" N LYS P 50 " --> pdb=" O THR P 39 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR P 36 " --> pdb=" O VAL P 22 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 9 through 16 removed outlier: 16.767A pdb=" N VAL Q 9 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) removed outlier: 13.353A pdb=" N TYR Q 30 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLN Q 11 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU Q 28 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR Q 24 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL Q 80 " --> pdb=" O ILE Q 60 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE Q 60 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 36 through 47 removed outlier: 5.820A pdb=" N ILE T 37 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN T 66 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY T 39 " --> pdb=" O ASN T 64 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR T 60 " --> pdb=" O TRP T 43 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS T 45 " --> pdb=" O GLY T 58 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY T 58 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG T 87 " --> pdb=" O ILE T 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 43 through 48 Processing sheet with id=AC8, first strand: chain 'E' and resid 20 through 21 removed outlier: 7.661A pdb=" N LYS E 21 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE E 56 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS E 53 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 68 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 147 through 152 removed outlier: 3.904A pdb=" N THR E 150 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR E 167 " --> pdb=" O THR E 150 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 179 through 189 removed outlier: 5.996A pdb=" N ASP E 180 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 73 through 78 Processing sheet with id=AD3, first strand: chain 'J' and resid 6 through 12 Processing sheet with id=AD4, first strand: chain 'K' and resid 35 through 55 removed outlier: 5.032A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 11 " --> pdb=" O ASP K 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 35 through 55 removed outlier: 5.032A pdb=" N VAL K 36 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL K 77 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY K 38 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP K 75 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS K 71 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR K 44 " --> pdb=" O THR K 69 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR K 69 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS K 46 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET K 67 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL K 48 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE K 65 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR K 50 " --> pdb=" O GLU K 63 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU K 63 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU K 52 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER K 61 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA K 54 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS K 59 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.301A pdb=" N VAL R 31 " --> pdb=" O ALA R 50 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TYR R 52 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR R 33 " --> pdb=" O TYR R 52 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1030 hydrogen bonds 1648 hydrogen bond angles 0 basepair planarities 414 basepair parallelities 771 stacking parallelities Total time for adding SS restraints: 33.52 Time building geometry restraints manager: 10.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11380 1.34 - 1.48: 22523 1.48 - 1.61: 21346 1.61 - 1.75: 362 1.75 - 1.88: 132 Bond restraints: 55743 Sorted by residual: bond pdb=" O3' C A 946 " pdb=" P A A 947 " ideal model delta sigma weight residual 1.607 1.680 -0.073 1.50e-02 4.44e+03 2.39e+01 bond pdb=" CA SER P 25 " pdb=" CB SER P 25 " ideal model delta sigma weight residual 1.528 1.459 0.069 1.56e-02 4.11e+03 1.97e+01 bond pdb=" C GLY F 34 " pdb=" N PRO F 35 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.63e+01 bond pdb=" O5' G A1046 " pdb=" C5' G A1046 " ideal model delta sigma weight residual 1.420 1.480 -0.060 1.50e-02 4.44e+03 1.59e+01 bond pdb=" CA SER S 77 " pdb=" CB SER S 77 " ideal model delta sigma weight residual 1.528 1.468 0.061 1.59e-02 3.96e+03 1.45e+01 ... (remaining 55738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 77682 3.28 - 6.57: 4018 6.57 - 9.85: 148 9.85 - 13.13: 18 13.13 - 16.42: 6 Bond angle restraints: 81872 Sorted by residual: angle pdb=" O3' A B9002 " pdb=" P A B9003 " pdb=" O5' A B9003 " ideal model delta sigma weight residual 104.00 87.58 16.42 1.50e+00 4.44e-01 1.20e+02 angle pdb=" OE1 GLN C 119 " pdb=" CD GLN C 119 " pdb=" NE2 GLN C 119 " ideal model delta sigma weight residual 122.60 132.21 -9.61 1.00e+00 1.00e+00 9.24e+01 angle pdb=" CA ASP T 76 " pdb=" CB ASP T 76 " pdb=" CG ASP T 76 " ideal model delta sigma weight residual 112.60 121.10 -8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA HIS L 35 " pdb=" CB HIS L 35 " pdb=" CG HIS L 35 " ideal model delta sigma weight residual 113.80 105.36 8.44 1.00e+00 1.00e+00 7.12e+01 angle pdb=" C LYS G 52 " pdb=" CA LYS G 52 " pdb=" CB LYS G 52 " ideal model delta sigma weight residual 109.75 123.48 -13.73 1.65e+00 3.67e-01 6.92e+01 ... (remaining 81867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 31907 35.74 - 71.49: 3071 71.49 - 107.23: 490 107.23 - 142.97: 23 142.97 - 178.71: 25 Dihedral angle restraints: 35516 sinusoidal: 27085 harmonic: 8431 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N LYS D 131 " pdb=" CA LYS D 131 " ideal model delta harmonic sigma weight residual -180.00 -94.28 -85.72 0 5.00e+00 4.00e-02 2.94e+02 dihedral pdb=" C5' C A 980 " pdb=" C4' C A 980 " pdb=" C3' C A 980 " pdb=" O3' C A 980 " ideal model delta sinusoidal sigma weight residual 147.00 65.10 81.90 1 8.00e+00 1.56e-02 1.29e+02 dihedral pdb=" CA LEU D 10 " pdb=" C LEU D 10 " pdb=" N GLU D 11 " pdb=" CA GLU D 11 " ideal model delta harmonic sigma weight residual 180.00 128.20 51.80 0 5.00e+00 4.00e-02 1.07e+02 ... (remaining 35513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 8771 0.161 - 0.322: 1486 0.322 - 0.483: 15 0.483 - 0.644: 3 0.644 - 0.805: 2 Chirality restraints: 10277 Sorted by residual: chirality pdb=" P A A 94 " pdb=" OP1 A A 94 " pdb=" OP2 A A 94 " pdb=" O5' A A 94 " both_signs ideal model delta sigma weight residual True 2.41 -3.22 -0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA LEU D 10 " pdb=" N LEU D 10 " pdb=" C LEU D 10 " pdb=" CB LEU D 10 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA PRO D 130 " pdb=" N PRO D 130 " pdb=" C PRO D 130 " pdb=" CB PRO D 130 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.69e+00 ... (remaining 10274 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 69 " 0.037 2.00e-02 2.50e+03 7.39e-02 5.47e+01 pdb=" C MET C 69 " -0.128 2.00e-02 2.50e+03 pdb=" O MET C 69 " 0.046 2.00e-02 2.50e+03 pdb=" N ASN C 70 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 69 " -0.545 9.50e-02 1.11e+02 2.45e-01 3.99e+01 pdb=" NE ARG L 69 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG L 69 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG L 69 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG L 69 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 33 " 0.477 9.50e-02 1.11e+02 2.14e-01 2.88e+01 pdb=" NE ARG J 33 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG J 33 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG J 33 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 33 " 0.011 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 13 2.26 - 2.92: 20706 2.92 - 3.58: 90388 3.58 - 4.24: 158065 4.24 - 4.90: 223109 Nonbonded interactions: 492281 Sorted by model distance: nonbonded pdb=" NE2 GLN C 119 " pdb=" CA ALA H 150 " model vdw 1.605 3.550 nonbonded pdb=" NE2 GLN C 119 " pdb=" N ALA H 150 " model vdw 1.611 3.200 nonbonded pdb=" OE1 GLN C 119 " pdb=" O LYS H 149 " model vdw 1.725 3.040 nonbonded pdb=" OE1 GLN C 119 " pdb=" C ALA H 150 " model vdw 1.856 3.270 nonbonded pdb=" CD GLN C 119 " pdb=" CA ALA H 150 " model vdw 1.860 3.700 ... (remaining 492276 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.390 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: 0.040 Extract box with map and model: 1.660 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 110.470 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 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 : 0.009 0.084 55743 Z= 0.582 Angle : 1.585 16.417 81872 Z= 1.018 Chirality : 0.109 0.805 10277 Planarity : 0.018 0.245 5424 Dihedral : 23.636 178.714 30066 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.38 % Favored : 92.89 % Rotamer: Outliers : 3.91 % Allowed : 6.02 % Favored : 90.07 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.39 % 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: -3.32 (0.13), residues: 2884 helix: -2.69 (0.11), residues: 1148 sheet: -1.90 (0.21), residues: 495 loop : -1.61 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.009 TRP E 200 HIS 0.030 0.004 HIS L 35 PHE 0.077 0.007 PHE O 15 TYR 0.054 0.007 TYR L 108 ARG 0.046 0.004 ARG F 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 578 time to evaluate : 2.512 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: C 11 LEU cc_start: 0.0729 (OUTLIER) cc_final: 0.0519 (mt) REVERT: C 230 MET cc_start: 0.1136 (mmm) cc_final: 0.0570 (ttp) REVERT: C 294 VAL cc_start: 0.4977 (t) cc_final: 0.4556 (p) REVERT: C 345 MET cc_start: 0.5007 (mtm) cc_final: 0.4806 (mtm) REVERT: C 347 ILE cc_start: 0.7635 (mt) cc_final: 0.7367 (mm) REVERT: C 370 THR cc_start: 0.4658 (p) cc_final: 0.4443 (t) REVERT: C 398 ASP cc_start: 0.2756 (m-30) cc_final: 0.2453 (m-30) REVERT: C 410 ARG cc_start: 0.7214 (ttp80) cc_final: 0.6527 (ttm-80) REVERT: C 495 TYR cc_start: 0.1063 (m-80) cc_final: 0.0608 (m-80) REVERT: C 618 LYS cc_start: 0.5044 (mmtt) cc_final: 0.4747 (mmmm) REVERT: C 660 MET cc_start: -0.0324 (mtp) cc_final: -0.1063 (mmm) REVERT: D 9 LEU cc_start: 0.4485 (mt) cc_final: 0.4258 (mt) REVERT: D 35 ARG cc_start: 0.6732 (ttt180) cc_final: 0.6315 (mtm-85) REVERT: D 113 ARG cc_start: 0.5641 (tpt170) cc_final: 0.5363 (mtt-85) REVERT: D 115 LYS cc_start: 0.6468 (mttt) cc_final: 0.6241 (mtpp) REVERT: D 178 LYS cc_start: 0.4483 (mttt) cc_final: 0.3799 (tttp) REVERT: D 180 ASN cc_start: 0.4832 (m-40) cc_final: 0.4596 (t0) REVERT: D 212 LEU cc_start: 0.7502 (tp) cc_final: 0.6973 (mm) REVERT: F 27 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7452 (tm-30) REVERT: F 28 LYS cc_start: 0.7734 (mttt) cc_final: 0.7140 (tptp) REVERT: F 29 ARG cc_start: 0.6438 (mtm180) cc_final: 0.5562 (mpt180) REVERT: F 30 PRO cc_start: 0.7657 (Cg_endo) cc_final: 0.7400 (Cg_exo) REVERT: F 64 ASN cc_start: 0.7009 (p0) cc_final: 0.6801 (p0) REVERT: F 66 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5263 (ptm160) REVERT: F 112 GLN cc_start: 0.7498 (tt0) cc_final: 0.7279 (tp-100) REVERT: F 144 LYS cc_start: 0.6694 (tttt) cc_final: 0.6193 (mmpt) REVERT: F 191 GLU cc_start: 0.7497 (pm20) cc_final: 0.6911 (pm20) REVERT: G 7 SER cc_start: 0.5707 (OUTLIER) cc_final: 0.5377 (p) REVERT: G 14 ARG cc_start: 0.7373 (ttp-170) cc_final: 0.6839 (mtp-110) REVERT: G 61 ARG cc_start: 0.5497 (ttp80) cc_final: 0.5195 (ttp-170) REVERT: G 76 MET cc_start: 0.7997 (mtm) cc_final: 0.7590 (mtp) REVERT: G 80 THR cc_start: 0.8001 (t) cc_final: 0.7672 (t) REVERT: G 116 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7478 (mt-10) REVERT: G 149 ARG cc_start: 0.6646 (ttm-80) cc_final: 0.6178 (tmm-80) REVERT: G 159 LYS cc_start: 0.7542 (mttm) cc_final: 0.7066 (tmtt) REVERT: I 10 MET cc_start: 0.7283 (ttt) cc_final: 0.6929 (tmm) REVERT: I 22 HIS cc_start: 0.7521 (m-70) cc_final: 0.7238 (m90) REVERT: I 26 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7056 (mt-10) REVERT: I 35 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6857 (mp0) REVERT: I 42 ARG cc_start: 0.7369 (ttm110) cc_final: 0.6694 (ptp-170) REVERT: I 113 LEU cc_start: 0.7090 (mt) cc_final: 0.6792 (mt) REVERT: I 122 GLN cc_start: 0.8070 (mp10) cc_final: 0.7459 (mt0) REVERT: L 32 LYS cc_start: 0.7189 (mmmt) cc_final: 0.6927 (mmtm) REVERT: L 62 LEU cc_start: 0.6108 (mt) cc_final: 0.5825 (mp) REVERT: L 68 VAL cc_start: 0.8461 (t) cc_final: 0.8219 (p) REVERT: L 91 SER cc_start: 0.7052 (m) cc_final: 0.6827 (t) REVERT: L 96 ARG cc_start: 0.6600 (ptt90) cc_final: 0.6358 (ptt90) REVERT: L 108 TYR cc_start: 0.7200 (m-80) cc_final: 0.6920 (m-10) REVERT: L 112 ARG cc_start: 0.6481 (mmm-85) cc_final: 0.6224 (mtp85) REVERT: L 120 VAL cc_start: 0.7887 (t) cc_final: 0.7559 (t) REVERT: L 123 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7809 (tpt-90) REVERT: O 26 GLU cc_start: 0.7258 (mp0) cc_final: 0.6884 (mp0) REVERT: O 81 LEU cc_start: 0.8103 (tp) cc_final: 0.7567 (tt) REVERT: O 88 ARG cc_start: 0.5363 (OUTLIER) cc_final: 0.4727 (ptm160) REVERT: P 77 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7195 (tp40) REVERT: Q 13 ARG cc_start: 0.7307 (ttp80) cc_final: 0.6490 (ttp-110) REVERT: Q 27 VAL cc_start: 0.8654 (t) cc_final: 0.8436 (m) REVERT: Q 41 LYS cc_start: 0.6830 (mtpt) cc_final: 0.6368 (mttp) REVERT: Q 77 LEU cc_start: 0.7067 (tp) cc_final: 0.6690 (tp) REVERT: Q 79 GLU cc_start: 0.6450 (mt-10) cc_final: 0.5854 (tt0) REVERT: Q 83 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: S 25 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6547 (ptpt) REVERT: S 32 ILE cc_start: 0.7779 (mt) cc_final: 0.7570 (mm) REVERT: S 33 LYS cc_start: 0.6881 (mtmt) cc_final: 0.6531 (tptt) REVERT: S 38 SER cc_start: 0.7977 (m) cc_final: 0.7436 (t) REVERT: S 42 ASN cc_start: 0.6241 (OUTLIER) cc_final: 0.4808 (p0) REVERT: S 52 THR cc_start: 0.8319 (p) cc_final: 0.8014 (t) REVERT: T 17 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6593 (mt-10) REVERT: T 41 LYS cc_start: 0.6529 (mttt) cc_final: 0.6197 (tptm) REVERT: T 67 SER cc_start: 0.7542 (p) cc_final: 0.7147 (t) REVERT: T 74 GLU cc_start: 0.7628 (tp30) cc_final: 0.7393 (mt-10) REVERT: U 17 TYR cc_start: 0.6254 (t80) cc_final: 0.5573 (t80) REVERT: U 24 THR cc_start: 0.6234 (p) cc_final: 0.6014 (m) REVERT: U 57 GLN cc_start: 0.7774 (tp40) cc_final: 0.7504 (tp40) REVERT: E 48 ASP cc_start: 0.4790 (OUTLIER) cc_final: 0.4536 (p0) REVERT: E 151 MET cc_start: 0.4968 (ttm) cc_final: 0.4502 (tpp) REVERT: E 163 ARG cc_start: 0.1923 (OUTLIER) cc_final: 0.1716 (tpp-160) REVERT: E 201 ILE cc_start: 0.4861 (mt) cc_final: 0.3615 (tp) REVERT: H 9 LYS cc_start: 0.1559 (OUTLIER) cc_final: 0.0330 (pptt) REVERT: H 15 ASP cc_start: 0.3552 (t70) cc_final: 0.3211 (p0) REVERT: H 63 GLU cc_start: 0.4658 (mt-10) cc_final: 0.4440 (tp30) REVERT: J 100 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.3854 (ptp-170) REVERT: R 53 ASP cc_start: 0.3669 (OUTLIER) cc_final: 0.3062 (t0) outliers start: 98 outliers final: 23 residues processed: 653 average time/residue: 0.6066 time to fit residues: 626.4732 Evaluate side-chains 446 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 411 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 0.9980 chunk 313 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 324 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 241 optimal weight: 0.0870 chunk 375 optimal weight: 5.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 360 GLN C 484 GLN D 123 ASN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN I 57 GLN I 68 GLN P 72 ASN P 84 HIS S 70 ASN T 61 GLN V 30 ASN V 42 ASN V 66 GLN E 133 GLN E 136 GLN H 64 GLN K 56 HIS K 64 GLN M 104 ASN M 105 ASN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55743 Z= 0.197 Angle : 0.768 24.729 81872 Z= 0.403 Chirality : 0.046 0.356 10277 Planarity : 0.005 0.067 5424 Dihedral : 23.968 179.074 24150 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.05 % Favored : 97.64 % Rotamer: Outliers : 0.24 % Allowed : 2.67 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2884 helix: 0.31 (0.14), residues: 1167 sheet: -1.30 (0.21), residues: 546 loop : -0.93 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 23 HIS 0.012 0.001 HIS K 56 PHE 0.031 0.002 PHE R 74 TYR 0.017 0.002 TYR D 90 ARG 0.008 0.001 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 485 time to evaluate : 2.592 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: symmetry clash REVERT: C 121 SER cc_start: 0.1222 (p) cc_final: 0.0988 (p) REVERT: C 230 MET cc_start: 0.0886 (mmm) cc_final: 0.0321 (ttp) REVERT: C 283 LEU cc_start: 0.7110 (tp) cc_final: 0.6655 (mp) REVERT: C 347 ILE cc_start: 0.7063 (mt) cc_final: 0.6245 (mm) REVERT: C 410 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6650 (ttm-80) REVERT: C 457 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4910 (tt0) REVERT: C 660 MET cc_start: -0.0567 (mtp) cc_final: -0.1183 (mmm) REVERT: D 43 LEU cc_start: 0.6115 (mt) cc_final: 0.5735 (tp) REVERT: D 178 LYS cc_start: 0.4810 (mttt) cc_final: 0.4117 (ttmm) REVERT: F 27 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7315 (tm-30) REVERT: F 28 LYS cc_start: 0.7674 (mttt) cc_final: 0.7027 (tptp) REVERT: F 29 ARG cc_start: 0.6306 (mtm180) cc_final: 0.5186 (mmt180) REVERT: F 30 PRO cc_start: 0.7747 (Cg_endo) cc_final: 0.7451 (Cg_exo) REVERT: F 47 TYR cc_start: 0.7227 (t80) cc_final: 0.6898 (t80) REVERT: F 51 LEU cc_start: 0.7987 (tp) cc_final: 0.7392 (tt) REVERT: F 94 LEU cc_start: 0.7600 (tp) cc_final: 0.7346 (tt) REVERT: F 138 THR cc_start: 0.5974 (m) cc_final: 0.5676 (t) REVERT: F 144 LYS cc_start: 0.6499 (tttt) cc_final: 0.6108 (mmpt) REVERT: F 189 ILE cc_start: 0.8451 (mm) cc_final: 0.8011 (mm) REVERT: G 14 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7165 (mtp-110) REVERT: G 61 ARG cc_start: 0.4916 (ttp80) cc_final: 0.4546 (ttp-170) REVERT: G 138 ARG cc_start: 0.6323 (mtt-85) cc_final: 0.6105 (ttm-80) REVERT: G 149 ARG cc_start: 0.6034 (ttm-80) cc_final: 0.5429 (mtm-85) REVERT: G 159 LYS cc_start: 0.7349 (mttm) cc_final: 0.7134 (tmtt) REVERT: I 9 ASP cc_start: 0.8189 (t0) cc_final: 0.7965 (t0) REVERT: I 22 HIS cc_start: 0.7468 (m-70) cc_final: 0.7266 (m170) REVERT: I 122 GLN cc_start: 0.7736 (mp10) cc_final: 0.7139 (mt0) REVERT: I 126 GLU cc_start: 0.8328 (tt0) cc_final: 0.7891 (tt0) REVERT: L 121 GLU cc_start: 0.6657 (tp30) cc_final: 0.5928 (pt0) REVERT: O 79 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7591 (mpt-90) REVERT: O 80 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6702 (tm-30) REVERT: O 88 ARG cc_start: 0.4411 (mpt-90) cc_final: 0.3308 (ptm160) REVERT: P 77 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6979 (tp40) REVERT: Q 13 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6529 (ttp-110) REVERT: Q 79 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6267 (tt0) REVERT: S 29 ARG cc_start: 0.7162 (mpp80) cc_final: 0.6679 (tpp80) REVERT: S 38 SER cc_start: 0.8151 (m) cc_final: 0.7913 (t) REVERT: T 41 LYS cc_start: 0.6321 (mttt) cc_final: 0.6081 (tptm) REVERT: U 57 GLN cc_start: 0.8026 (tp40) cc_final: 0.7697 (tp40) REVERT: V 67 MET cc_start: 0.1459 (mtp) cc_final: 0.0920 (tpp) REVERT: E 149 LYS cc_start: 0.4933 (tttt) cc_final: 0.4310 (tppt) REVERT: E 151 MET cc_start: 0.4672 (ttm) cc_final: 0.4032 (tmm) REVERT: H 63 GLU cc_start: 0.4548 (mt-10) cc_final: 0.4338 (tp30) outliers start: 6 outliers final: 0 residues processed: 490 average time/residue: 0.5793 time to fit residues: 458.0618 Evaluate side-chains 390 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 312 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 406 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN C 333 ASN C 670 GLN D 136 GLN F 55 GLN F 67 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 ASN I 110 GLN L 109 HIS L 125 GLN P 72 ASN Q 53 ASN U 25 HIS E 136 GLN H 56 ASN ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 55743 Z= 0.289 Angle : 0.789 9.536 81872 Z= 0.411 Chirality : 0.046 0.476 10277 Planarity : 0.006 0.079 5424 Dihedral : 23.969 179.597 24150 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.43 % Favored : 96.26 % Rotamer: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2884 helix: 0.68 (0.14), residues: 1172 sheet: -1.05 (0.21), residues: 507 loop : -0.85 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 43 HIS 0.009 0.002 HIS I 22 PHE 0.027 0.004 PHE R 74 TYR 0.027 0.002 TYR E 202 ARG 0.014 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 458 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 MET cc_start: 0.0996 (mmm) cc_final: 0.0682 (ttp) REVERT: C 294 VAL cc_start: 0.4668 (t) cc_final: 0.4290 (p) REVERT: C 347 ILE cc_start: 0.6852 (mt) cc_final: 0.6611 (mp) REVERT: C 485 LYS cc_start: 0.4683 (mmtp) cc_final: 0.4477 (pttt) REVERT: C 495 TYR cc_start: 0.2536 (m-80) cc_final: 0.2146 (m-80) REVERT: C 660 MET cc_start: -0.1317 (mtp) cc_final: -0.1580 (mmm) REVERT: D 42 ASP cc_start: 0.3712 (t0) cc_final: 0.3390 (t0) REVERT: D 113 ARG cc_start: 0.6278 (tpm170) cc_final: 0.5738 (mmt180) REVERT: D 114 LEU cc_start: 0.5717 (tp) cc_final: 0.5482 (mp) REVERT: D 178 LYS cc_start: 0.5247 (mttt) cc_final: 0.4532 (tttt) REVERT: F 9 TRP cc_start: 0.5209 (m-10) cc_final: 0.4964 (m-10) REVERT: F 27 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7239 (tm-30) REVERT: F 28 LYS cc_start: 0.7609 (mttt) cc_final: 0.6909 (tptp) REVERT: F 29 ARG cc_start: 0.6637 (mtm180) cc_final: 0.5433 (mmt180) REVERT: F 30 PRO cc_start: 0.7802 (Cg_endo) cc_final: 0.7550 (Cg_exo) REVERT: F 47 TYR cc_start: 0.7299 (t80) cc_final: 0.6843 (t80) REVERT: F 51 LEU cc_start: 0.7892 (tp) cc_final: 0.7570 (tt) REVERT: F 55 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: F 138 THR cc_start: 0.5859 (m) cc_final: 0.5656 (t) REVERT: F 189 ILE cc_start: 0.8317 (mm) cc_final: 0.7950 (mp) REVERT: F 190 ASN cc_start: 0.7893 (t0) cc_final: 0.7498 (t0) REVERT: G 14 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7212 (mtp-110) REVERT: G 30 ARG cc_start: 0.7306 (mmm-85) cc_final: 0.6744 (ptm160) REVERT: G 61 ARG cc_start: 0.5362 (ttp80) cc_final: 0.5074 (ttp-170) REVERT: G 138 ARG cc_start: 0.6545 (mtt-85) cc_final: 0.6315 (mtt180) REVERT: G 149 ARG cc_start: 0.6156 (ttm-80) cc_final: 0.5955 (tmm-80) REVERT: G 159 LYS cc_start: 0.7457 (mttm) cc_final: 0.7150 (tmtt) REVERT: I 9 ASP cc_start: 0.8370 (t0) cc_final: 0.8101 (t0) REVERT: I 77 LEU cc_start: 0.8028 (mp) cc_final: 0.7793 (mt) REVERT: I 122 GLN cc_start: 0.7917 (mp10) cc_final: 0.7450 (mt0) REVERT: I 126 GLU cc_start: 0.8088 (tt0) cc_final: 0.7825 (tt0) REVERT: L 125 GLN cc_start: 0.7701 (mt0) cc_final: 0.7237 (mp10) REVERT: L 129 LYS cc_start: 0.6763 (mtpt) cc_final: 0.6411 (mttp) REVERT: O 31 ILE cc_start: 0.8553 (mm) cc_final: 0.8290 (mm) REVERT: O 64 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7248 (ttp-110) REVERT: O 87 LEU cc_start: 0.6961 (mt) cc_final: 0.6756 (mt) REVERT: O 88 ARG cc_start: 0.4081 (mpt-90) cc_final: 0.3066 (ptm160) REVERT: P 77 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6957 (tp40) REVERT: Q 13 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6350 (ttp-110) REVERT: Q 79 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7124 (mm-30) REVERT: S 29 ARG cc_start: 0.7075 (mpp80) cc_final: 0.6630 (tpp80) REVERT: T 41 LYS cc_start: 0.6455 (mttt) cc_final: 0.6064 (tptm) REVERT: U 46 PRO cc_start: 0.6821 (Cg_exo) cc_final: 0.6469 (Cg_endo) REVERT: U 57 GLN cc_start: 0.8206 (tp40) cc_final: 0.7688 (tp40) REVERT: V 67 MET cc_start: 0.1804 (mtp) cc_final: 0.1217 (tpp) REVERT: E 149 LYS cc_start: 0.5142 (tttt) cc_final: 0.4634 (tppt) REVERT: H 59 MET cc_start: 0.1987 (mtp) cc_final: 0.1739 (mtm) REVERT: H 63 GLU cc_start: 0.4360 (mt-10) cc_final: 0.3953 (tp30) outliers start: 4 outliers final: 0 residues processed: 462 average time/residue: 0.5864 time to fit residues: 435.3007 Evaluate side-chains 383 residues out of total 2507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1008 > 50: distance: 16 - 34: 28.852 distance: 20 - 46: 20.775 distance: 27 - 34: 26.678 distance: 34 - 35: 39.863 distance: 35 - 36: 16.519 distance: 35 - 38: 17.994 distance: 36 - 37: 36.906 distance: 36 - 46: 46.390 distance: 38 - 39: 42.804 distance: 39 - 40: 10.353 distance: 39 - 41: 9.518 distance: 40 - 42: 23.173 distance: 41 - 43: 25.997 distance: 42 - 44: 21.878 distance: 43 - 44: 23.153 distance: 44 - 45: 18.873 distance: 46 - 47: 14.843 distance: 47 - 48: 15.718 distance: 47 - 50: 44.791 distance: 48 - 49: 25.144 distance: 48 - 54: 8.934 distance: 50 - 51: 29.012 distance: 51 - 52: 26.673 distance: 52 - 53: 32.813 distance: 54 - 55: 26.348 distance: 55 - 56: 24.343 distance: 55 - 58: 48.406 distance: 56 - 57: 22.034 distance: 56 - 62: 29.007 distance: 58 - 59: 36.104 distance: 59 - 60: 18.472 distance: 59 - 61: 38.021 distance: 62 - 63: 15.749 distance: 63 - 64: 22.343 distance: 63 - 66: 15.674 distance: 64 - 65: 20.646 distance: 64 - 70: 9.349 distance: 66 - 67: 13.916 distance: 67 - 68: 29.615 distance: 67 - 69: 11.642 distance: 70 - 71: 16.713 distance: 71 - 72: 31.485 distance: 71 - 74: 21.655 distance: 72 - 73: 12.373 distance: 72 - 79: 24.610 distance: 74 - 75: 28.727 distance: 75 - 76: 8.785 distance: 76 - 77: 5.706 distance: 77 - 78: 9.956 distance: 79 - 80: 30.692 distance: 80 - 81: 28.247 distance: 80 - 83: 4.817 distance: 81 - 82: 26.743 distance: 81 - 87: 34.923 distance: 83 - 84: 31.547 distance: 83 - 85: 39.613 distance: 84 - 86: 25.671 distance: 87 - 88: 27.903 distance: 88 - 89: 20.584 distance: 89 - 90: 13.460 distance: 89 - 91: 23.111 distance: 91 - 92: 61.101 distance: 92 - 93: 32.344 distance: 92 - 95: 32.820 distance: 93 - 94: 10.211 distance: 93 - 100: 8.784 distance: 95 - 96: 60.341 distance: 96 - 97: 15.038 distance: 97 - 98: 21.701 distance: 97 - 99: 19.399 distance: 100 - 101: 44.726 distance: 101 - 102: 29.212 distance: 101 - 104: 14.256 distance: 102 - 103: 46.412 distance: 102 - 109: 30.286 distance: 104 - 105: 28.569 distance: 105 - 106: 30.965 distance: 106 - 107: 33.839 distance: 106 - 108: 35.871 distance: 109 - 110: 27.969 distance: 109 - 149: 18.230 distance: 110 - 111: 28.208 distance: 110 - 113: 19.467 distance: 111 - 112: 12.806 distance: 111 - 120: 20.773 distance: 112 - 146: 22.381 distance: 113 - 114: 30.124 distance: 114 - 115: 21.544 distance: 114 - 116: 18.830 distance: 115 - 117: 16.528 distance: 116 - 118: 8.569 distance: 117 - 119: 22.258 distance: 118 - 119: 19.088