Starting phenix.real_space_refine on Sat Dec 9 21:21:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nma_0445/12_2023/6nma_0445.pdb" } resolution = 3.38 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= 0.004 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: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 7870 2.51 5 N 2049 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 737": "NH1" <-> "NH2" Residue "B GLU 743": "OE1" <-> "OE2" Residue "B ARG 747": "NH1" <-> "NH2" Residue "B TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B GLU 981": "OE1" <-> "OE2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "B GLU 1117": "OE1" <-> "OE2" Residue "B GLU 1171": "OE1" <-> "OE2" Residue "B GLU 1202": "OE1" <-> "OE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12404 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "B" Number of atoms: 9974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9974 Classifications: {'peptide': 1206} Link IDs: {'PTRANS': 25, 'TRANS': 1180} Chain breaks: 4 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 942 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.04, per 1000 atoms: 0.57 Number of scatterers: 12404 At special positions: 0 Unit cell: (126.854, 108.732, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 25 15.00 Mg 2 11.99 O 2417 8.00 N 2049 7.00 C 7870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 45.4% alpha, 9.7% beta 6 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 120 through 125 removed outlier: 4.091A pdb=" N VAL A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 125' Processing helix chain 'A' and resid 126 through 129 removed outlier: 5.018A pdb=" N ARG A 129 " --> pdb=" O ALA A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.715A pdb=" N LYS A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.636A pdb=" N ARG A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.688A pdb=" N ASN B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 66 removed outlier: 3.638A pdb=" N ALA B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLY B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 4.385A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 104 removed outlier: 3.984A pdb=" N LEU B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.644A pdb=" N GLU B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.889A pdb=" N GLU B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 removed outlier: 4.038A pdb=" N VAL B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.645A pdb=" N VAL B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 3.779A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.522A pdb=" N ILE B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 312 through 327 Processing helix chain 'B' and resid 341 through 351 removed outlier: 4.134A pdb=" N SER B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 removed outlier: 3.561A pdb=" N ASP B 360 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.809A pdb=" N PHE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 437' Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.721A pdb=" N SER B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.738A pdb=" N ASP B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.597A pdb=" N ARG B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 588 through 598 Proline residue: B 594 - end of helix Processing helix chain 'B' and resid 610 through 619 Processing helix chain 'B' and resid 629 through 644 removed outlier: 4.005A pdb=" N HIS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 718 through 727 removed outlier: 3.516A pdb=" N MET B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 811 through 822 removed outlier: 3.941A pdb=" N ARG B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.808A pdb=" N GLU B 885 " --> pdb=" O LYS B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 900 Processing helix chain 'B' and resid 907 through 919 removed outlier: 3.813A pdb=" N LEU B 914 " --> pdb=" O LYS B 910 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU B 916 " --> pdb=" O CYS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 930 removed outlier: 4.265A pdb=" N GLY B 930 " --> pdb=" O LEU B 927 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 930' Processing helix chain 'B' and resid 939 through 948 removed outlier: 3.819A pdb=" N LYS B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 955 Processing helix chain 'B' and resid 1020 through 1031 removed outlier: 3.645A pdb=" N SER B1024 " --> pdb=" O SER B1020 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 removed outlier: 3.597A pdb=" N TYR B1102 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1120 through 1135 removed outlier: 4.468A pdb=" N TYR B1124 " --> pdb=" O ASP B1120 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B1128 " --> pdb=" O TYR B1124 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B1129 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B1135 " --> pdb=" O MET B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1167 Processing helix chain 'B' and resid 1180 through 1199 removed outlier: 3.671A pdb=" N LYS B1190 " --> pdb=" O ASN B1186 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B1191 " --> pdb=" O ILE B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1209 Processing helix chain 'B' and resid 1214 through 1225 Processing helix chain 'C' and resid 123 through 149 removed outlier: 3.733A pdb=" N ALA C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.980A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.589A pdb=" N VAL A 207 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.168A pdb=" N TYR B 794 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.666A pdb=" N ARG B 737 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA6, first strand: chain 'B' and resid 552 through 556 removed outlier: 4.923A pdb=" N ILE B 546 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 581 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 758 through 759 removed outlier: 3.551A pdb=" N VAL B 783 " --> pdb=" O HIS B 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 850 through 855 removed outlier: 3.539A pdb=" N GLU B 852 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU B 925 " --> pdb=" O ILE B 831 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 922 " --> pdb=" O PHE B 994 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 996 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 924 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 858 through 863 Processing sheet with id=AB1, first strand: chain 'B' and resid 1033 through 1037 removed outlier: 3.544A pdb=" N LEU B1042 " --> pdb=" O VAL B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1070 through 1073 Processing sheet with id=AB3, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.467A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2341 1.32 - 1.44: 3250 1.44 - 1.57: 7003 1.57 - 1.69: 49 1.69 - 1.81: 67 Bond restraints: 12710 Sorted by residual: bond pdb=" N SER B 855 " pdb=" CA SER B 855 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.18e+00 bond pdb=" N GLU B 882 " pdb=" CA GLU B 882 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.65e+00 bond pdb=" CA GLN B 975 " pdb=" CB GLN B 975 " ideal model delta sigma weight residual 1.527 1.459 0.068 2.48e-02 1.63e+03 7.48e+00 bond pdb=" N LEU B 856 " pdb=" CA LEU B 856 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N ARG B1112 " pdb=" CA ARG B1112 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.64e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.65: 281 105.65 - 112.74: 6561 112.74 - 119.84: 4624 119.84 - 126.93: 5603 126.93 - 134.03: 155 Bond angle restraints: 17224 Sorted by residual: angle pdb=" N ILE B 904 " pdb=" CA ILE B 904 " pdb=" C ILE B 904 " ideal model delta sigma weight residual 111.91 107.11 4.80 8.90e-01 1.26e+00 2.91e+01 angle pdb=" N ILE B1141 " pdb=" CA ILE B1141 " pdb=" C ILE B1141 " ideal model delta sigma weight residual 113.53 109.79 3.74 9.80e-01 1.04e+00 1.45e+01 angle pdb=" C ASN C 169 " pdb=" N LEU C 170 " pdb=" CA LEU C 170 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N GLY B 902 " pdb=" CA GLY B 902 " pdb=" C GLY B 902 " ideal model delta sigma weight residual 113.18 105.36 7.82 2.37e+00 1.78e-01 1.09e+01 angle pdb=" N ILE B1111 " pdb=" CA ILE B1111 " pdb=" C ILE B1111 " ideal model delta sigma weight residual 111.91 109.04 2.87 8.90e-01 1.26e+00 1.04e+01 ... (remaining 17219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 7430 32.08 - 64.17: 246 64.17 - 96.25: 27 96.25 - 128.33: 0 128.33 - 160.42: 1 Dihedral angle restraints: 7704 sinusoidal: 3437 harmonic: 4267 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 71.58 160.42 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" CA ASN B 933 " pdb=" C ASN B 933 " pdb=" N SER B 934 " pdb=" CA SER B 934 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ARG B 86 " pdb=" C ARG B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1271 0.048 - 0.096: 509 0.096 - 0.144: 77 0.144 - 0.192: 7 0.192 - 0.240: 1 Chirality restraints: 1865 Sorted by residual: chirality pdb=" C1' C G 11 " pdb=" O4' C G 11 " pdb=" C2' C G 11 " pdb=" N1 C G 11 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B1111 " pdb=" N ILE B1111 " pdb=" C ILE B1111 " pdb=" CB ILE B1111 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B1034 " pdb=" N ILE B1034 " pdb=" C ILE B1034 " pdb=" CB ILE B1034 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 1862 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C G 11 " 0.027 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 C G 11 " -0.037 2.00e-02 2.50e+03 pdb=" C2 C G 11 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C G 11 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C G 11 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C G 11 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C G 11 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C G 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 21 " -0.029 2.00e-02 2.50e+03 1.23e-02 4.17e+00 pdb=" N9 A G 21 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A G 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 A G 21 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A G 21 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A G 21 " -0.007 2.00e-02 2.50e+03 pdb=" N6 A G 21 " -0.012 2.00e-02 2.50e+03 pdb=" N1 A G 21 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A G 21 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A G 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A G 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 193 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 194 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 141 2.56 - 3.14: 10455 3.14 - 3.73: 18256 3.73 - 4.31: 26135 4.31 - 4.90: 42863 Nonbonded interactions: 97850 Sorted by model distance: nonbonded pdb=" NZ LYS A 202 " pdb="MG MG A 301 " model vdw 1.973 2.250 nonbonded pdb=" OP2 A G 19 " pdb="MG MG G1301 " model vdw 2.020 2.170 nonbonded pdb=" O THR B1055 " pdb=" OG1 THR B1055 " model vdw 2.104 2.440 nonbonded pdb=" O THR B 246 " pdb=" OG1 THR B 246 " model vdw 2.197 2.440 nonbonded pdb=" O LYS B 595 " pdb=" OG SER B 599 " model vdw 2.200 2.440 ... (remaining 97845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 120 through 233) selection = chain 'C' } 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 individual isotropic 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: 0.950 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: 3.570 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 38.860 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.078 12710 Z= 0.600 Angle : 0.780 7.816 17224 Z= 0.455 Chirality : 0.048 0.240 1865 Planarity : 0.004 0.049 2110 Dihedral : 15.679 160.416 4952 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.98 % Favored : 88.95 % Rotamer: Outliers : 8.09 % Allowed : 10.46 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.17), residues: 1421 helix: -2.79 (0.16), residues: 586 sheet: -3.82 (0.33), residues: 163 loop : -3.58 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 534 HIS 0.006 0.001 HIS A 190 PHE 0.017 0.002 PHE B 61 TYR 0.024 0.002 TYR B 294 ARG 0.005 0.001 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 212 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 61 residues processed: 298 average time/residue: 0.2578 time to fit residues: 108.4928 Evaluate side-chains 219 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 158 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.1277 time to fit residues: 15.7094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN A 168 ASN A 208 ASN B 33 ASN B 63 ASN B 157 ASN B 263 ASN B 567 GLN B 651 ASN B 676 GLN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS B 808 ASN B 861 ASN B 864 ASN B 906 GLN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12710 Z= 0.173 Angle : 0.550 6.553 17224 Z= 0.294 Chirality : 0.042 0.159 1865 Planarity : 0.004 0.045 2110 Dihedral : 10.617 167.178 1906 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.21 % Allowed : 16.26 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.21), residues: 1421 helix: -1.22 (0.20), residues: 593 sheet: -3.57 (0.32), residues: 174 loop : -2.75 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 999 HIS 0.004 0.001 HIS B 759 PHE 0.028 0.001 PHE B 131 TYR 0.020 0.001 TYR B1036 ARG 0.005 0.000 ARG B1112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 217 average time/residue: 0.2311 time to fit residues: 74.1273 Evaluate side-chains 175 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1515 time to fit residues: 5.5616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12710 Z= 0.171 Angle : 0.509 6.871 17224 Z= 0.273 Chirality : 0.041 0.151 1865 Planarity : 0.003 0.044 2110 Dihedral : 10.503 172.803 1906 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.52 % Allowed : 18.17 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 1421 helix: -0.38 (0.22), residues: 592 sheet: -3.23 (0.35), residues: 158 loop : -2.52 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.002 0.001 HIS A 190 PHE 0.023 0.001 PHE B 225 TYR 0.013 0.001 TYR B 294 ARG 0.004 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 218 average time/residue: 0.2367 time to fit residues: 76.2777 Evaluate side-chains 187 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1166 time to fit residues: 5.4956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12710 Z= 0.264 Angle : 0.554 9.993 17224 Z= 0.290 Chirality : 0.042 0.166 1865 Planarity : 0.003 0.045 2110 Dihedral : 10.514 173.087 1906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.06 % Allowed : 19.77 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1421 helix: -0.26 (0.22), residues: 601 sheet: -3.11 (0.35), residues: 170 loop : -2.34 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.003 0.001 HIS A 190 PHE 0.026 0.001 PHE B 244 TYR 0.015 0.001 TYR B 294 ARG 0.003 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.451 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 191 average time/residue: 0.2340 time to fit residues: 66.9664 Evaluate side-chains 178 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1453 time to fit residues: 5.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12710 Z= 0.239 Angle : 0.543 9.849 17224 Z= 0.284 Chirality : 0.042 0.168 1865 Planarity : 0.003 0.043 2110 Dihedral : 10.468 173.745 1906 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.07 % Allowed : 20.69 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.22), residues: 1421 helix: 0.05 (0.22), residues: 595 sheet: -3.03 (0.36), residues: 167 loop : -2.25 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS A 190 PHE 0.033 0.001 PHE B 244 TYR 0.014 0.001 TYR B 294 ARG 0.003 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.477 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 182 average time/residue: 0.2418 time to fit residues: 65.2857 Evaluate side-chains 164 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1249 time to fit residues: 3.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12710 Z= 0.299 Angle : 0.565 9.632 17224 Z= 0.295 Chirality : 0.043 0.169 1865 Planarity : 0.003 0.044 2110 Dihedral : 10.483 172.772 1906 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.37 % Allowed : 21.45 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1421 helix: 0.10 (0.22), residues: 601 sheet: -2.99 (0.35), residues: 171 loop : -2.16 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 999 HIS 0.003 0.001 HIS A 190 PHE 0.029 0.001 PHE B 244 TYR 0.016 0.001 TYR B 294 ARG 0.008 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.421 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 168 average time/residue: 0.2352 time to fit residues: 58.5457 Evaluate side-chains 165 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1230 time to fit residues: 4.8458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 0.0030 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12710 Z= 0.190 Angle : 0.525 10.856 17224 Z= 0.274 Chirality : 0.041 0.175 1865 Planarity : 0.003 0.041 2110 Dihedral : 10.405 174.604 1906 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.84 % Allowed : 21.98 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1421 helix: 0.37 (0.23), residues: 594 sheet: -2.91 (0.37), residues: 157 loop : -2.13 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 999 HIS 0.003 0.001 HIS A 190 PHE 0.031 0.001 PHE B 244 TYR 0.017 0.001 TYR B 678 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.477 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 171 average time/residue: 0.2411 time to fit residues: 61.6806 Evaluate side-chains 154 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1327 time to fit residues: 3.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12710 Z= 0.160 Angle : 0.515 8.997 17224 Z= 0.268 Chirality : 0.040 0.165 1865 Planarity : 0.003 0.038 2110 Dihedral : 10.345 176.364 1906 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.92 % Allowed : 21.98 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1421 helix: 0.56 (0.23), residues: 594 sheet: -2.80 (0.38), residues: 143 loop : -2.11 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1086 HIS 0.003 0.001 HIS A 190 PHE 0.028 0.001 PHE B 225 TYR 0.015 0.001 TYR B 678 ARG 0.005 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.856 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 170 average time/residue: 0.2885 time to fit residues: 72.4499 Evaluate side-chains 157 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1421 time to fit residues: 3.4120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 67.7987 > 50: distance: 32 - 152: 25.969 distance: 60 - 82: 28.846 distance: 74 - 99: 29.298 distance: 78 - 82: 28.908 distance: 82 - 83: 50.233 distance: 83 - 84: 57.866 distance: 83 - 86: 46.423 distance: 84 - 85: 29.075 distance: 84 - 91: 41.991 distance: 85 - 115: 15.901 distance: 86 - 87: 34.797 distance: 87 - 88: 17.598 distance: 88 - 89: 11.609 distance: 88 - 90: 18.310 distance: 91 - 92: 53.057 distance: 92 - 93: 67.799 distance: 92 - 95: 35.830 distance: 93 - 94: 54.062 distance: 93 - 99: 66.118 distance: 94 - 124: 24.956 distance: 95 - 96: 21.789 distance: 96 - 97: 14.366 distance: 96 - 98: 17.853 distance: 99 - 100: 45.814 distance: 100 - 101: 15.530 distance: 100 - 103: 36.361 distance: 101 - 102: 18.231 distance: 101 - 106: 32.784 distance: 102 - 136: 33.641 distance: 103 - 104: 15.582 distance: 103 - 105: 27.856 distance: 106 - 107: 23.893 distance: 107 - 108: 39.068 distance: 107 - 110: 11.875 distance: 108 - 109: 47.004 distance: 108 - 115: 44.938 distance: 110 - 111: 21.234 distance: 111 - 112: 7.561 distance: 112 - 114: 23.286 distance: 115 - 116: 41.913 distance: 116 - 117: 34.282 distance: 116 - 119: 41.614 distance: 117 - 118: 34.887 distance: 117 - 124: 45.382 distance: 119 - 120: 11.245 distance: 120 - 121: 10.955 distance: 121 - 122: 9.738 distance: 122 - 123: 33.750 distance: 124 - 125: 33.167 distance: 125 - 126: 9.725 distance: 125 - 128: 29.813 distance: 126 - 127: 31.397 distance: 126 - 136: 3.099 distance: 128 - 129: 16.085 distance: 129 - 130: 32.022 distance: 129 - 131: 9.808 distance: 130 - 132: 4.885 distance: 131 - 133: 14.893 distance: 132 - 134: 13.811 distance: 133 - 134: 10.583 distance: 134 - 135: 17.735 distance: 136 - 137: 26.013 distance: 137 - 138: 18.339 distance: 137 - 140: 20.309 distance: 138 - 139: 17.471 distance: 138 - 144: 23.580 distance: 140 - 141: 8.368 distance: 141 - 142: 8.611 distance: 141 - 143: 19.440 distance: 144 - 145: 27.205 distance: 145 - 146: 51.567 distance: 145 - 148: 31.641 distance: 146 - 147: 42.567 distance: 146 - 149: 36.045 distance: 149 - 150: 46.867 distance: 150 - 151: 53.353 distance: 150 - 153: 50.013 distance: 151 - 152: 37.349 distance: 151 - 156: 22.858 distance: 153 - 154: 26.225 distance: 153 - 155: 33.607 distance: 156 - 157: 41.569 distance: 157 - 158: 58.470 distance: 157 - 160: 43.364 distance: 158 - 159: 59.095 distance: 158 - 164: 34.113 distance: 160 - 161: 7.544 distance: 160 - 162: 4.802 distance: 161 - 163: 32.997