Starting phenix.real_space_refine (version: dev) on Tue Mar 14 19:33:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w01_32233/03_2023/7w01_32233_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 655": "OE1" <-> "OE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ASP 689": "OD1" <-> "OD2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 957": "NH1" <-> "NH2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A ASP 1058": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1149": "OD1" <-> "OD2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1180": "OD1" <-> "OD2" Residue "A PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1325": "OE1" <-> "OE2" Residue "A GLU 1385": "OE1" <-> "OE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A ASP 1400": "OD1" <-> "OD2" Residue "A PHE 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1446": "NH1" <-> "NH2" Residue "A ARG 1457": "NH1" <-> "NH2" Residue "A PHE 1464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1474": "NH1" <-> "NH2" Residue "A ARG 1482": "NH1" <-> "NH2" Residue "A ARG 1484": "NH1" <-> "NH2" Residue "A ARG 1489": "NH1" <-> "NH2" Residue "A ARG 1513": "NH1" <-> "NH2" Residue "A ARG 1521": "NH1" <-> "NH2" Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1551": "NH1" <-> "NH2" Residue "A GLU 1576": "OE1" <-> "OE2" Residue "A TYR 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1641": "OE1" <-> "OE2" Residue "A GLU 1667": "OE1" <-> "OE2" Residue "A GLU 1671": "OE1" <-> "OE2" Residue "A TYR 1673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1689": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 12724 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1605, 12724 Unusual residues: {'NAG': 2, 'POV': 3, 'PX4': 2} Classifications: {'peptide': 1598, 'undetermined': 7} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 74, 'TRANS': 1523, None: 7} Not linked: pdbres="PRO A1698 " pdbres="NAG A1801 " Not linked: pdbres="NAG A1801 " pdbres="NAG A1802 " Not linked: pdbres="NAG A1802 " pdbres="PX4 A1803 " Not linked: pdbres="PX4 A1803 " pdbres="PX4 A1804 " Not linked: pdbres="PX4 A1804 " pdbres="POV A1805 " ... (remaining 2 not shown) Chain breaks: 5 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'POV:plan-2': 3, 'POV:plan-3': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Time building chain proxies: 8.32, per 1000 atoms: 0.65 Number of scatterers: 12724 At special positions: 0 Unit cell: (102.6, 142.56, 141.48, 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 70 16.00 P 2 15.00 O 2251 8.00 N 2114 7.00 C 8287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1274 " - pdb=" SG CYS A1284 " distance=2.03 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 Links applied NAG-ASN " NAG A1801 " - " ASN A 124 " " NAG A1802 " - " ASN A 140 " Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 42.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 removed outlier: 3.548A pdb=" N ALA A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.549A pdb=" N THR A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 4.137A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.728A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 3.663A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.694A pdb=" N ALA A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.590A pdb=" N MET A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 327 removed outlier: 3.560A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.705A pdb=" N CYS A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 401 through 409 removed outlier: 4.187A pdb=" N LEU A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.610A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 473 removed outlier: 3.742A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 601 through 606 removed outlier: 4.528A pdb=" N LYS A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.810A pdb=" N LEU A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'A' and resid 670 through 679 removed outlier: 3.541A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.784A pdb=" N ILE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.695A pdb=" N LYS A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.502A pdb=" N GLN A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 806 through 815 removed outlier: 3.796A pdb=" N LYS A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.511A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 removed outlier: 3.694A pdb=" N TRP A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.512A pdb=" N THR A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 989 removed outlier: 3.614A pdb=" N ALA A 989 " --> pdb=" O HIS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 removed outlier: 3.560A pdb=" N ILE A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1022 No H-bonds generated for 'chain 'A' and resid 1019 through 1022' Processing helix chain 'A' and resid 1049 through 1064 removed outlier: 4.018A pdb=" N LEU A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1089 removed outlier: 3.501A pdb=" N ALA A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.640A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1115 removed outlier: 3.880A pdb=" N PHE A1115 " --> pdb=" O ALA A1112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1112 through 1115' Processing helix chain 'A' and resid 1118 through 1124 removed outlier: 3.902A pdb=" N ARG A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1134 removed outlier: 3.598A pdb=" N GLN A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1153 removed outlier: 3.935A pdb=" N TRP A1142 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1166 removed outlier: 4.490A pdb=" N LEU A1161 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1178 through 1202 removed outlier: 3.859A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Proline residue: A1194 - end of helix removed outlier: 3.916A pdb=" N ASN A1200 " --> pdb=" O MET A1196 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A1201 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A1202 " --> pdb=" O LEU A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1229 removed outlier: 3.914A pdb=" N TYR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1223 " --> pdb=" O LEU A1219 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1248 removed outlier: 3.665A pdb=" N LYS A1243 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A1246 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1273 removed outlier: 3.518A pdb=" N MET A1259 " --> pdb=" O HIS A1255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A1260 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A1263 " --> pdb=" O MET A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1287 Processing helix chain 'A' and resid 1307 through 1311 Processing helix chain 'A' and resid 1316 through 1325 removed outlier: 3.819A pdb=" N LEU A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1367 Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.827A pdb=" N PHE A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1482 removed outlier: 3.820A pdb=" N LEU A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A1480 " --> pdb=" O MET A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1501 removed outlier: 3.696A pdb=" N THR A1498 " --> pdb=" O CYS A1494 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1507 No H-bonds generated for 'chain 'A' and resid 1505 through 1507' Processing helix chain 'A' and resid 1511 through 1513 No H-bonds generated for 'chain 'A' and resid 1511 through 1513' Processing helix chain 'A' and resid 1521 through 1524 No H-bonds generated for 'chain 'A' and resid 1521 through 1524' Processing helix chain 'A' and resid 1547 through 1562 removed outlier: 3.861A pdb=" N THR A1556 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1561 " --> pdb=" O VAL A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1579 No H-bonds generated for 'chain 'A' and resid 1576 through 1579' Processing helix chain 'A' and resid 1598 through 1605 Processing helix chain 'A' and resid 1620 through 1633 removed outlier: 5.252A pdb=" N GLU A1625 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1672 removed outlier: 4.685A pdb=" N GLU A1671 " --> pdb=" O GLU A1667 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A1672 " --> pdb=" O LYS A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1695 removed outlier: 3.556A pdb=" N SER A1691 " --> pdb=" O GLN A1687 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A1692 " --> pdb=" O VAL A1688 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA A1693 " --> pdb=" O PHE A1689 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N HIS A1694 " --> pdb=" O LEU A1690 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A1695 " --> pdb=" O SER A1691 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.131A pdb=" N THR A1036 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR A 241 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A1038 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 243 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A1040 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A1035 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1037 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.546A pdb=" N ARG A 108 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA A 81 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 132 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.092A pdb=" N SER A1071 " --> pdb=" O VAL A 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.803A pdb=" N LEU A 556 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 741 through 745 removed outlier: 6.902A pdb=" N ILE A 735 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS A 744 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 733 " --> pdb=" O CYS A 744 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 732 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 716 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY A 609 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1410 through 1412 Processing sheet with id= G, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.413A pdb=" N LYS A 537 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 550 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1386 through 1391 removed outlier: 3.506A pdb=" N LEU A1386 " --> pdb=" O ARG A1401 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A1388 " --> pdb=" O VAL A1399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A1399 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A1390 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A1397 " --> pdb=" O TYR A1390 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 6.14 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: 3948 1.34 - 1.46: 2625 1.46 - 1.58: 6334 1.58 - 1.70: 4 1.70 - 1.82: 115 Bond restraints: 13026 Sorted by residual: bond pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C29 POV A1805 " pdb="C210 POV A1805 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C9 PX4 A1804 " pdb=" O5 PX4 A1804 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C9 PX4 A1803 " pdb=" O5 PX4 A1803 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 13021 not shown) Histogram of bond angle deviations from ideal: 96.14 - 104.02: 211 104.02 - 111.90: 6132 111.90 - 119.77: 5255 119.77 - 127.65: 5901 127.65 - 135.53: 129 Bond angle restraints: 17628 Sorted by residual: angle pdb=" C ILE A1233 " pdb=" N PRO A1234 " pdb=" CA PRO A1234 " ideal model delta sigma weight residual 119.84 128.00 -8.16 1.25e+00 6.40e-01 4.26e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" C ARG A 155 " ideal model delta sigma weight residual 110.80 123.93 -13.13 2.13e+00 2.20e-01 3.80e+01 angle pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " ideal model delta sigma weight residual 116.84 127.00 -10.16 1.71e+00 3.42e-01 3.53e+01 angle pdb=" C28 POV A1806 " pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 127.79 110.77 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C28 POV A1807 " pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 127.79 110.91 16.88 3.00e+00 1.11e-01 3.17e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 7523 33.87 - 67.73: 193 67.73 - 101.60: 17 101.60 - 135.47: 3 135.47 - 169.34: 1 Dihedral angle restraints: 7737 sinusoidal: 3101 harmonic: 4636 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " ideal model delta harmonic sigma weight residual 180.00 126.71 53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASN A 140 " pdb=" C ASN A 140 " pdb=" N HIS A 141 " pdb=" CA HIS A 141 " ideal model delta harmonic sigma weight residual -180.00 -136.79 -43.21 0 5.00e+00 4.00e-02 7.47e+01 dihedral pdb=" CA PHE A 156 " pdb=" C PHE A 156 " pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta harmonic sigma weight residual 180.00 147.42 32.58 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1934 0.134 - 0.269: 45 0.269 - 0.403: 1 0.403 - 0.537: 0 0.537 - 0.672: 1 Chirality restraints: 1981 Sorted by residual: chirality pdb=" CA PHE A 156 " pdb=" N PHE A 156 " pdb=" C PHE A 156 " pdb=" CB PHE A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA PHE A1172 " pdb=" N PHE A1172 " pdb=" C PHE A1172 " pdb=" CB PHE A1172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C7 PX4 A1804 " pdb=" C6 PX4 A1804 " pdb=" C8 PX4 A1804 " pdb=" O7 PX4 A1804 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1978 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1805 " 0.159 2.00e-02 2.50e+03 3.23e-01 1.04e+03 pdb=" C29 POV A1805 " -0.428 2.00e-02 2.50e+03 pdb="C210 POV A1805 " 0.428 2.00e-02 2.50e+03 pdb="C211 POV A1805 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1806 " -0.321 2.00e-02 2.50e+03 3.22e-01 1.04e+03 pdb=" C29 POV A1806 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV A1806 " 0.328 2.00e-02 2.50e+03 pdb="C211 POV A1806 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1807 " -0.102 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C29 POV A1807 " 0.101 2.00e-02 2.50e+03 pdb="C210 POV A1807 " 0.104 2.00e-02 2.50e+03 pdb="C211 POV A1807 " -0.103 2.00e-02 2.50e+03 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 19 2.35 - 2.99: 6714 2.99 - 3.63: 17059 3.63 - 4.26: 26808 4.26 - 4.90: 45812 Nonbonded interactions: 96412 Sorted by model distance: nonbonded pdb=" O VAL A 968 " pdb=" O GLN A 995 " model vdw 1.717 3.040 nonbonded pdb=" O THR A 966 " pdb=" CB GLU A 993 " model vdw 2.030 3.440 nonbonded pdb=" NE2 GLN A 613 " pdb=" OE1 GLU A 690 " model vdw 2.074 2.520 nonbonded pdb=" OD2 ASP A1149 " pdb=" OH TYR A1197 " model vdw 2.076 2.440 nonbonded pdb=" O LYS A 711 " pdb=" N ASP A 713 " model vdw 2.202 2.520 ... (remaining 96407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 8287 2.51 5 N 2114 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.660 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: 4.190 Check model and map are aligned: 0.190 Process input model: 38.060 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.011 0.190 13026 Z= 0.751 Angle : 1.106 17.015 17628 Z= 0.578 Chirality : 0.060 0.672 1981 Planarity : 0.011 0.323 2216 Dihedral : 15.952 169.336 4742 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.30 % Favored : 85.94 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.26 % 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: -4.55 (0.19), residues: 1586 helix: -2.52 (0.16), residues: 794 sheet: -3.42 (0.41), residues: 134 loop : -3.47 (0.21), residues: 658 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.659 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 0.3110 time to fit residues: 72.8732 Evaluate side-chains 136 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2819 time to fit residues: 4.0291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 ASN A1490 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13026 Z= 0.183 Angle : 0.686 13.304 17628 Z= 0.342 Chirality : 0.043 0.264 1981 Planarity : 0.005 0.073 2216 Dihedral : 11.011 166.790 1820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.77 % Favored : 89.85 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.90 (0.19), residues: 1586 helix: -1.95 (0.17), residues: 792 sheet: -3.07 (0.41), residues: 136 loop : -3.20 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.562 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 164 average time/residue: 0.2666 time to fit residues: 63.6057 Evaluate side-chains 146 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1222 time to fit residues: 3.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13026 Z= 0.226 Angle : 0.648 11.450 17628 Z= 0.321 Chirality : 0.043 0.207 1981 Planarity : 0.005 0.070 2216 Dihedral : 10.529 168.785 1820 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.66 % Favored : 89.03 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.49 (0.20), residues: 1586 helix: -1.59 (0.18), residues: 795 sheet: -2.66 (0.43), residues: 134 loop : -3.10 (0.23), residues: 657 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.604 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.2709 time to fit residues: 64.4425 Evaluate side-chains 149 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1181 time to fit residues: 4.2494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1076 ASN A1687 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13026 Z= 0.167 Angle : 0.609 14.025 17628 Z= 0.299 Chirality : 0.042 0.200 1981 Planarity : 0.004 0.067 2216 Dihedral : 10.171 170.879 1820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.52 % Favored : 90.23 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.17 (0.20), residues: 1586 helix: -1.28 (0.18), residues: 789 sheet: -2.52 (0.43), residues: 132 loop : -3.00 (0.23), residues: 665 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.420 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 167 average time/residue: 0.2632 time to fit residues: 64.3225 Evaluate side-chains 148 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1213 time to fit residues: 3.8428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13026 Z= 0.180 Angle : 0.603 13.060 17628 Z= 0.296 Chirality : 0.041 0.182 1981 Planarity : 0.004 0.062 2216 Dihedral : 10.039 173.888 1820 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.95 % Favored : 90.73 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.95 (0.21), residues: 1586 helix: -1.08 (0.18), residues: 791 sheet: -2.32 (0.43), residues: 132 loop : -2.94 (0.23), residues: 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.565 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 169 average time/residue: 0.2959 time to fit residues: 72.5343 Evaluate side-chains 152 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1168 time to fit residues: 3.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13026 Z= 0.261 Angle : 0.637 12.882 17628 Z= 0.311 Chirality : 0.043 0.179 1981 Planarity : 0.005 0.059 2216 Dihedral : 10.124 179.960 1820 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.28 % Favored : 89.47 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.87 (0.21), residues: 1586 helix: -1.03 (0.18), residues: 794 sheet: -2.17 (0.43), residues: 138 loop : -2.92 (0.23), residues: 654 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.541 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 161 average time/residue: 0.2891 time to fit residues: 66.8743 Evaluate side-chains 149 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1249 time to fit residues: 4.9047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 62.7454 > 50: distance: 71 - 98: 24.644 distance: 85 - 90: 13.613 distance: 90 - 91: 6.976 distance: 91 - 92: 18.574 distance: 91 - 94: 14.197 distance: 92 - 93: 20.293 distance: 92 - 98: 30.430 distance: 94 - 95: 18.247 distance: 95 - 96: 13.033 distance: 95 - 97: 11.551 distance: 98 - 99: 6.997 distance: 99 - 100: 13.432 distance: 99 - 102: 30.866 distance: 100 - 101: 28.144 distance: 100 - 109: 44.579 distance: 102 - 103: 15.752 distance: 103 - 104: 45.993 distance: 104 - 105: 12.181 distance: 105 - 106: 16.111 distance: 106 - 107: 12.008 distance: 106 - 108: 15.157 distance: 109 - 110: 16.299 distance: 110 - 111: 4.403 distance: 110 - 113: 41.637 distance: 111 - 112: 21.441 distance: 111 - 117: 33.784 distance: 113 - 114: 12.605 distance: 114 - 115: 22.181 distance: 114 - 116: 18.244 distance: 117 - 118: 14.982 distance: 118 - 119: 22.793 distance: 118 - 121: 25.078 distance: 119 - 120: 15.808 distance: 119 - 123: 25.451 distance: 121 - 122: 5.007 distance: 123 - 124: 8.570 distance: 124 - 125: 6.443 distance: 124 - 127: 17.403 distance: 125 - 126: 22.759 distance: 125 - 131: 21.705 distance: 127 - 128: 22.136 distance: 128 - 129: 29.287 distance: 128 - 130: 15.604 distance: 131 - 132: 33.472 distance: 132 - 133: 31.369 distance: 132 - 135: 15.780 distance: 133 - 134: 47.829 distance: 133 - 136: 30.332 distance: 136 - 137: 25.353 distance: 137 - 138: 15.734 distance: 137 - 140: 14.318 distance: 138 - 139: 22.736 distance: 138 - 143: 11.538 distance: 140 - 141: 14.705 distance: 140 - 142: 24.462 distance: 143 - 144: 14.503 distance: 144 - 145: 23.891 distance: 144 - 147: 30.782 distance: 145 - 146: 13.888 distance: 145 - 152: 22.064 distance: 147 - 148: 9.146 distance: 148 - 149: 10.032 distance: 149 - 150: 6.649 distance: 149 - 151: 5.553 distance: 152 - 153: 9.621 distance: 153 - 154: 32.445 distance: 153 - 156: 26.509 distance: 154 - 155: 17.126 distance: 154 - 161: 23.432 distance: 156 - 157: 22.516 distance: 157 - 158: 18.709 distance: 158 - 159: 13.052 distance: 159 - 160: 35.543 distance: 161 - 162: 46.726 distance: 162 - 163: 23.650 distance: 163 - 164: 34.318 distance: 163 - 165: 17.567