Starting phenix.real_space_refine on Mon Mar 18 19:49:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1r_15803/03_2024/8b1r_15803.pdb" } resolution = 3.2 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 100 5.16 5 C 13863 2.51 5 N 3860 2.21 5 O 4129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ASP 798": "OD1" <-> "OD2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 823": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 902": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 923": "NH1" <-> "NH2" Residue "B ARG 974": "NH1" <-> "NH2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B ARG 1015": "NH1" <-> "NH2" Residue "B GLU 1020": "OE1" <-> "OE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1149": "OE1" <-> "OE2" Residue "B PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C GLU 559": "OE1" <-> "OE2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ARG 649": "NH1" <-> "NH2" Residue "C ARG 653": "NH1" <-> "NH2" Residue "C PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 1040": "OE1" <-> "OE2" Residue "C ARG 1068": "NH1" <-> "NH2" Residue "C ASP 1087": "OD1" <-> "OD2" Residue "C PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "Q TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21953 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9358 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 52, 'TRANS': 1117} Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2706 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain: "P" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "Q" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "B" 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: 11.70, per 1000 atoms: 0.53 Number of scatterers: 21953 At special positions: 0 Unit cell: (104.5, 136.4, 155.1, 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 100 16.00 Mg 1 11.99 O 4129 8.00 N 3860 7.00 C 13863 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: 8.02 Conformation dependent library (CDL) restraints added in 4.1 seconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 18 sheets defined 58.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.608A pdb=" N THR B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.759A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.024A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.647A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.907A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.637A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.521A pdb=" N VAL B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.633A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.550A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.800A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 482 through 487 removed outlier: 4.161A pdb=" N ALA B 486 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.772A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.510A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.897A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.590A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.625A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 removed outlier: 3.701A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.031A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.685A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.680A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 808 " --> pdb=" O VAL B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 835 removed outlier: 4.144A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 844 Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 961 removed outlier: 3.667A pdb=" N ASP B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.686A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 997 " --> pdb=" O TRP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 4.061A pdb=" N GLN B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1050 Processing helix chain 'B' and resid 1089 through 1093 Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.025A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1161 through 1174 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.989A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.618A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.760A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 104 through 107 removed outlier: 6.241A pdb=" N ASP C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.770A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.682A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix removed outlier: 3.801A pdb=" N HIS C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.409A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 4.066A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.034A pdb=" N LEU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 287' Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.745A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.669A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.712A pdb=" N GLU C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.637A pdb=" N VAL C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.899A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 580 removed outlier: 3.719A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 573 " --> pdb=" O MET C 569 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN C 580 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 removed outlier: 3.608A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 598 " --> pdb=" O MET C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.185A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 648 removed outlier: 3.972A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.592A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 700' Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.885A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 794 Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.827A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.938A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.649A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.881A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.631A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 933 " --> pdb=" O ASP C 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 removed outlier: 3.543A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1077 Processing helix chain 'C' and resid 1087 through 1094 Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 71 removed outlier: 3.698A pdb=" N ALA D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.606A pdb=" N CYS D 84 " --> pdb=" O ASN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.578A pdb=" N ALA D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 221 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.528A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 233 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.500A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.678A pdb=" N ASP D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.563A pdb=" N VAL D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.895A pdb=" N ASN D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'P' and resid 10 through 49 removed outlier: 3.557A pdb=" N ASN P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP P 15 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 49 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.228A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.637A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.516A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 581 removed outlier: 3.855A pdb=" N GLN B 737 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR B 749 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 812 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 751 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER B 814 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP B 753 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY B 816 " --> pdb=" O TRP B 753 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 904 through 905 removed outlier: 9.749A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 904 through 905 removed outlier: 6.699A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.425A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN C 264 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP C 324 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.045A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.418A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 375 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.724A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.845A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 956 " --> pdb=" O MET C 941 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C 941 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.845A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 14.768A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C1004 " --> pdb=" O LEU C1000 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.533A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.508A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.825A pdb=" N SER D 238 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 203 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 5 through 9 removed outlier: 3.543A pdb=" N ILE Q 8 " --> pdb=" O VAL P 6 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3324 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: 8.24 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6514 1.34 - 1.45: 3410 1.45 - 1.57: 12336 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 22428 Sorted by residual: bond pdb=" N PRO B 283 " pdb=" CD PRO B 283 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" N HIS B 307 " pdb=" CA HIS B 307 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 1.445 1.475 -0.031 9.90e-03 1.02e+04 9.67e+00 bond pdb=" N TRP B 401 " pdb=" CA TRP B 401 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.55e+00 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.15: 775 107.15 - 113.94: 12464 113.94 - 120.74: 10187 120.74 - 127.54: 6750 127.54 - 134.34: 266 Bond angle restraints: 30442 Sorted by residual: angle pdb=" N LEU B1002 " pdb=" CA LEU B1002 " pdb=" C LEU B1002 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 angle pdb=" N ASN B1003 " pdb=" CA ASN B1003 " pdb=" C ASN B1003 " ideal model delta sigma weight residual 108.45 114.50 -6.05 1.26e+00 6.30e-01 2.31e+01 angle pdb=" N LEU C 600 " pdb=" CA LEU C 600 " pdb=" C LEU C 600 " ideal model delta sigma weight residual 108.69 100.69 8.00 1.80e+00 3.09e-01 1.97e+01 angle pdb=" N PHE C 599 " pdb=" CA PHE C 599 " pdb=" C PHE C 599 " ideal model delta sigma weight residual 109.24 116.59 -7.35 1.67e+00 3.59e-01 1.94e+01 angle pdb=" N PHE C 326 " pdb=" CA PHE C 326 " pdb=" C PHE C 326 " ideal model delta sigma weight residual 110.24 115.82 -5.58 1.41e+00 5.03e-01 1.57e+01 ... (remaining 30437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 12887 14.97 - 29.94: 561 29.94 - 44.92: 107 44.92 - 59.89: 28 59.89 - 74.86: 9 Dihedral angle restraints: 13592 sinusoidal: 5586 harmonic: 8006 Sorted by residual: dihedral pdb=" CA LYS B 256 " pdb=" C LYS B 256 " pdb=" N PHE B 257 " pdb=" CA PHE B 257 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ARG C 433 " pdb=" CB ARG C 433 " pdb=" CG ARG C 433 " pdb=" CD ARG C 433 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2776 0.055 - 0.109: 409 0.109 - 0.164: 117 0.164 - 0.219: 34 0.219 - 0.274: 6 Chirality restraints: 3342 Sorted by residual: chirality pdb=" CA VAL Q 6 " pdb=" N VAL Q 6 " pdb=" C VAL Q 6 " pdb=" CB VAL Q 6 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL C 547 " pdb=" CA VAL C 547 " pdb=" CG1 VAL C 547 " pdb=" CG2 VAL C 547 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE Q 8 " pdb=" N ILE Q 8 " pdb=" C ILE Q 8 " pdb=" CB ILE Q 8 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3339 not shown) Planarity restraints: 4015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO C 658 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 3 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ARG P 3 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG P 3 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP P 4 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 295 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLU B 295 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU B 295 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 296 " -0.010 2.00e-02 2.50e+03 ... (remaining 4012 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2327 2.75 - 3.29: 21026 3.29 - 3.82: 35086 3.82 - 4.36: 41171 4.36 - 4.90: 72963 Nonbonded interactions: 172573 Sorted by model distance: nonbonded pdb=" OG1 THR B 63 " pdb=" OG1 THR B 69 " model vdw 2.210 2.440 nonbonded pdb=" NH2 ARG B 254 " pdb=" OE2 GLU Q 45 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR B 906 " pdb=" O ARG B1106 " model vdw 2.229 2.440 nonbonded pdb=" O TYR B1081 " pdb="MG MG B1301 " model vdw 2.286 2.170 ... (remaining 172568 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 'P' selection = chain 'Q' } 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: 0.560 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: 0.020 Extract box with map and model: 3.900 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 58.670 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 : 0.004 0.063 22428 Z= 0.274 Angle : 0.633 7.998 30442 Z= 0.455 Chirality : 0.047 0.274 3342 Planarity : 0.004 0.055 4015 Dihedral : 9.184 74.859 8398 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.34 % Allowed : 3.50 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 0.06 (0.15), residues: 2736 helix: 0.48 (0.13), residues: 1456 sheet: 0.80 (0.32), residues: 224 loop : -0.62 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 236 HIS 0.004 0.001 HIS B 402 PHE 0.013 0.001 PHE C 193 TYR 0.020 0.001 TYR B1111 ARG 0.003 0.000 ARG C 734 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 409 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 VAL cc_start: 0.9309 (t) cc_final: 0.8362 (m) REVERT: B 289 PHE cc_start: 0.8826 (m-80) cc_final: 0.8153 (m-80) REVERT: B 310 PHE cc_start: 0.8229 (m-80) cc_final: 0.7924 (m-80) REVERT: B 469 MET cc_start: 0.8942 (ptm) cc_final: 0.8707 (ptm) REVERT: B 518 MET cc_start: 0.9282 (mmm) cc_final: 0.8948 (mmm) REVERT: B 541 MET cc_start: 0.8150 (mtp) cc_final: 0.7888 (mtm) REVERT: B 902 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8256 (ptt-90) REVERT: B 941 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8094 (t) REVERT: B 1102 MET cc_start: 0.8747 (mmm) cc_final: 0.8453 (mmm) REVERT: C 484 ASP cc_start: 0.8611 (t0) cc_final: 0.8324 (t0) REVERT: C 698 SER cc_start: 0.9307 (t) cc_final: 0.9054 (p) REVERT: C 1031 MET cc_start: 0.9096 (mmt) cc_final: 0.8804 (mmp) REVERT: C 1078 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 348 LEU cc_start: 0.8699 (tp) cc_final: 0.8481 (tp) REVERT: P 24 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8656 (mt-10) REVERT: P 33 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8305 (tm-30) REVERT: Q 15 ASP cc_start: 0.8465 (m-30) cc_final: 0.8071 (m-30) REVERT: Q 40 TYR cc_start: 0.8062 (t80) cc_final: 0.7859 (t80) outliers start: 8 outliers final: 3 residues processed: 415 average time/residue: 0.4237 time to fit residues: 254.8425 Evaluate side-chains 212 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1078 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 258 ASN B 403 HIS B 594 GLN C 137 GLN C 264 GLN C 960 GLN C1073 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Q 14 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22428 Z= 0.323 Angle : 0.539 7.594 30442 Z= 0.277 Chirality : 0.040 0.175 3342 Planarity : 0.004 0.050 4015 Dihedral : 3.738 49.150 3024 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.49 % Allowed : 7.33 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 1.37 (0.15), residues: 2736 helix: 1.73 (0.13), residues: 1455 sheet: 1.29 (0.33), residues: 210 loop : -0.26 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 13 HIS 0.004 0.001 HIS B 772 PHE 0.018 0.002 PHE C 193 TYR 0.026 0.002 TYR B1111 ARG 0.008 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 PHE cc_start: 0.8169 (t80) cc_final: 0.7917 (t80) REVERT: B 321 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 469 MET cc_start: 0.8999 (ptm) cc_final: 0.8786 (ptm) REVERT: B 541 MET cc_start: 0.8333 (mtp) cc_final: 0.8014 (mtp) REVERT: B 788 ASP cc_start: 0.8287 (m-30) cc_final: 0.8066 (m-30) REVERT: B 823 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6653 (mmm-85) REVERT: B 902 ARG cc_start: 0.8581 (ptt180) cc_final: 0.8233 (ptt-90) REVERT: B 1021 MET cc_start: 0.8921 (ttm) cc_final: 0.8651 (ttp) REVERT: B 1102 MET cc_start: 0.8759 (mmm) cc_final: 0.8403 (mmm) REVERT: C 266 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7569 (ptm160) REVERT: C 281 GLU cc_start: 0.8030 (mp0) cc_final: 0.7703 (mp0) REVERT: D 218 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6687 (mmtm) REVERT: P 28 ASP cc_start: 0.8798 (m-30) cc_final: 0.8501 (m-30) REVERT: P 31 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8462 (mmtm) REVERT: Q 30 LEU cc_start: 0.8725 (mm) cc_final: 0.8410 (mt) outliers start: 35 outliers final: 13 residues processed: 232 average time/residue: 0.3624 time to fit residues: 128.9597 Evaluate side-chains 193 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 0.0770 chunk 76 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 198 optimal weight: 10.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1057 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22428 Z= 0.193 Angle : 0.470 13.479 30442 Z= 0.236 Chirality : 0.038 0.160 3342 Planarity : 0.004 0.054 4015 Dihedral : 3.505 39.730 3019 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.28 % Allowed : 8.44 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 1.86 (0.15), residues: 2736 helix: 2.22 (0.13), residues: 1459 sheet: 1.35 (0.33), residues: 210 loop : -0.18 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 616 HIS 0.003 0.001 HIS B 222 PHE 0.015 0.001 PHE C 193 TYR 0.023 0.001 TYR B1111 ARG 0.008 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B 390 ASP cc_start: 0.7701 (t0) cc_final: 0.7448 (t0) REVERT: B 469 MET cc_start: 0.8969 (ptm) cc_final: 0.8765 (ptm) REVERT: B 541 MET cc_start: 0.8287 (mtp) cc_final: 0.7883 (mtp) REVERT: B 788 ASP cc_start: 0.8268 (m-30) cc_final: 0.8052 (m-30) REVERT: B 823 ARG cc_start: 0.7052 (ttm170) cc_final: 0.6578 (mmm-85) REVERT: B 902 ARG cc_start: 0.8557 (ptt180) cc_final: 0.8213 (ptt-90) REVERT: B 1021 MET cc_start: 0.8880 (ttm) cc_final: 0.8627 (ttp) REVERT: B 1102 MET cc_start: 0.8776 (mmm) cc_final: 0.8401 (mmm) REVERT: C 266 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7151 (ttt90) REVERT: C 281 GLU cc_start: 0.7995 (mp0) cc_final: 0.7670 (mp0) REVERT: C 288 ASN cc_start: 0.7827 (t0) cc_final: 0.7595 (m-40) REVERT: D 61 ASN cc_start: 0.8036 (m-40) cc_final: 0.7823 (m110) REVERT: D 218 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6756 (mmtm) REVERT: P 10 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8465 (tpt170) REVERT: Q 24 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8165 (mt-10) REVERT: Q 33 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8049 (mm-40) outliers start: 30 outliers final: 16 residues processed: 206 average time/residue: 0.3462 time to fit residues: 111.0363 Evaluate side-chains 191 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 941 MET Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1078 ASN Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 33 GLN Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 ASN C 522 HIS C 724 GLN C 881 ASN C 920 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 22428 Z= 0.487 Angle : 0.596 13.139 30442 Z= 0.304 Chirality : 0.043 0.161 3342 Planarity : 0.005 0.053 4015 Dihedral : 4.026 39.929 3019 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.88 % Allowed : 8.32 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 1.64 (0.15), residues: 2736 helix: 2.07 (0.13), residues: 1462 sheet: 1.20 (0.33), residues: 213 loop : -0.31 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 616 HIS 0.006 0.001 HIS B 440 PHE 0.021 0.002 PHE B 774 TYR 0.028 0.002 TYR B1111 ARG 0.009 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 2.640 Fit side-chains REVERT: B 321 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 541 MET cc_start: 0.8588 (mtp) cc_final: 0.8262 (mtp) REVERT: B 902 ARG cc_start: 0.8578 (ptt180) cc_final: 0.8236 (ptt-90) REVERT: B 1021 MET cc_start: 0.8930 (ttm) cc_final: 0.8690 (ttp) REVERT: B 1102 MET cc_start: 0.8832 (mmm) cc_final: 0.8388 (mmm) REVERT: C 266 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7268 (ttt90) REVERT: C 281 GLU cc_start: 0.8065 (mp0) cc_final: 0.7726 (mp0) REVERT: C 288 ASN cc_start: 0.7827 (t0) cc_final: 0.7580 (m-40) REVERT: C 667 MET cc_start: 0.9374 (mmt) cc_final: 0.9038 (mmt) REVERT: C 962 ASP cc_start: 0.8185 (t0) cc_final: 0.7783 (t0) REVERT: D 184 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7706 (mm) REVERT: D 218 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6586 (mmmt) REVERT: Q 24 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8180 (mt-10) outliers start: 44 outliers final: 25 residues processed: 209 average time/residue: 0.3416 time to fit residues: 111.8794 Evaluate side-chains 193 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1078 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 224 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 235 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 ASN C 881 ASN C 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22428 Z= 0.126 Angle : 0.450 14.326 30442 Z= 0.226 Chirality : 0.037 0.157 3342 Planarity : 0.004 0.044 4015 Dihedral : 3.566 37.279 3019 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.15 % Allowed : 9.30 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.12 (0.16), residues: 2736 helix: 2.50 (0.14), residues: 1462 sheet: 1.30 (0.34), residues: 215 loop : -0.12 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 616 HIS 0.003 0.000 HIS C 377 PHE 0.013 0.001 PHE C 193 TYR 0.022 0.001 TYR B1111 ARG 0.010 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8837 (pp) REVERT: B 541 MET cc_start: 0.8482 (mtp) cc_final: 0.8187 (mtp) REVERT: B 788 ASP cc_start: 0.8280 (m-30) cc_final: 0.8072 (m-30) REVERT: B 823 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6410 (mmm-85) REVERT: B 902 ARG cc_start: 0.8499 (ptt180) cc_final: 0.8228 (ptt-90) REVERT: B 1102 MET cc_start: 0.8746 (mmm) cc_final: 0.7981 (mtp) REVERT: C 266 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7240 (ttt90) REVERT: C 281 GLU cc_start: 0.8010 (mp0) cc_final: 0.7642 (mp0) REVERT: C 667 MET cc_start: 0.9342 (mmt) cc_final: 0.9041 (mmt) REVERT: C 962 ASP cc_start: 0.8013 (t0) cc_final: 0.7575 (t0) REVERT: D 218 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6549 (mmmt) REVERT: P 19 TYR cc_start: 0.8858 (t80) cc_final: 0.8637 (t80) REVERT: Q 17 GLN cc_start: 0.9295 (mm110) cc_final: 0.9049 (mm-40) REVERT: Q 24 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8051 (mt-10) outliers start: 27 outliers final: 12 residues processed: 207 average time/residue: 0.3483 time to fit residues: 112.0676 Evaluate side-chains 186 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 154 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 881 ASN C 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22428 Z= 0.254 Angle : 0.487 13.254 30442 Z= 0.245 Chirality : 0.038 0.133 3342 Planarity : 0.004 0.055 4015 Dihedral : 3.625 37.846 3019 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.15 % Allowed : 9.51 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.13 (0.16), residues: 2736 helix: 2.49 (0.14), residues: 1475 sheet: 1.32 (0.33), residues: 218 loop : -0.14 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 616 HIS 0.003 0.001 HIS B 440 PHE 0.025 0.001 PHE B 31 TYR 0.023 0.001 TYR B1111 ARG 0.010 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 PHE cc_start: 0.8075 (t80) cc_final: 0.7853 (t80) REVERT: B 321 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8829 (pp) REVERT: B 541 MET cc_start: 0.8497 (mtp) cc_final: 0.8188 (mtp) REVERT: B 788 ASP cc_start: 0.8331 (m-30) cc_final: 0.8081 (m-30) REVERT: B 823 ARG cc_start: 0.6791 (ttm170) cc_final: 0.6374 (mmm-85) REVERT: B 902 ARG cc_start: 0.8536 (ptt180) cc_final: 0.8249 (ptt-90) REVERT: B 1102 MET cc_start: 0.8752 (mmm) cc_final: 0.8506 (mtp) REVERT: C 266 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7287 (ttt90) REVERT: C 281 GLU cc_start: 0.8079 (mp0) cc_final: 0.7719 (mp0) REVERT: C 962 ASP cc_start: 0.8075 (t0) cc_final: 0.7655 (t0) REVERT: C 1017 LEU cc_start: 0.9296 (mt) cc_final: 0.9051 (mt) REVERT: D 218 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6629 (mmmt) REVERT: P 36 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8945 (tm-30) REVERT: Q 3 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7932 (mmm160) REVERT: Q 17 GLN cc_start: 0.9305 (mm110) cc_final: 0.9062 (mm-40) REVERT: Q 24 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8026 (mt-10) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.3814 time to fit residues: 114.7211 Evaluate side-chains 187 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 10.0000 chunk 29 optimal weight: 0.0000 chunk 149 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 chunk 262 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1110 GLN C 881 ASN C 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22428 Z= 0.121 Angle : 0.443 15.384 30442 Z= 0.221 Chirality : 0.036 0.145 3342 Planarity : 0.003 0.045 4015 Dihedral : 3.411 34.329 3019 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.15 % Allowed : 9.89 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.32 (0.16), residues: 2736 helix: 2.64 (0.14), residues: 1472 sheet: 1.34 (0.34), residues: 223 loop : -0.02 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 265 HIS 0.002 0.000 HIS C 185 PHE 0.022 0.001 PHE B 31 TYR 0.021 0.001 TYR B1111 ARG 0.010 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8804 (pp) REVERT: B 541 MET cc_start: 0.8462 (mtp) cc_final: 0.8135 (mtp) REVERT: B 823 ARG cc_start: 0.6829 (ttm170) cc_final: 0.6385 (mmm-85) REVERT: B 902 ARG cc_start: 0.8496 (ptt180) cc_final: 0.8210 (ptt-90) REVERT: B 1061 MET cc_start: 0.8751 (mmt) cc_final: 0.8526 (mmt) REVERT: C 266 ARG cc_start: 0.7835 (ptm160) cc_final: 0.7280 (ttt90) REVERT: C 281 GLU cc_start: 0.8069 (mp0) cc_final: 0.7797 (mp0) REVERT: C 962 ASP cc_start: 0.7941 (t0) cc_final: 0.7473 (t0) REVERT: C 1017 LEU cc_start: 0.9258 (mt) cc_final: 0.9026 (mt) REVERT: D 218 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6609 (mmmt) REVERT: P 1 MET cc_start: 0.5374 (mtt) cc_final: 0.5053 (mtt) REVERT: Q 3 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7865 (mmm160) REVERT: Q 17 GLN cc_start: 0.9304 (mm110) cc_final: 0.9101 (mm110) outliers start: 27 outliers final: 15 residues processed: 198 average time/residue: 0.3616 time to fit residues: 110.2361 Evaluate side-chains 188 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 881 ASN C 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22428 Z= 0.204 Angle : 0.466 12.676 30442 Z= 0.233 Chirality : 0.037 0.133 3342 Planarity : 0.004 0.056 4015 Dihedral : 3.449 34.959 3018 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.11 % Allowed : 10.19 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.32 (0.16), residues: 2736 helix: 2.63 (0.14), residues: 1470 sheet: 1.32 (0.34), residues: 223 loop : -0.01 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 265 HIS 0.003 0.001 HIS C 185 PHE 0.025 0.001 PHE B 31 TYR 0.022 0.001 TYR B1111 ARG 0.012 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 541 MET cc_start: 0.8526 (mtp) cc_final: 0.8214 (mtp) REVERT: B 823 ARG cc_start: 0.7008 (ttm170) cc_final: 0.6529 (mmm-85) REVERT: B 902 ARG cc_start: 0.8542 (ptt180) cc_final: 0.8236 (ptt-90) REVERT: C 266 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7293 (ttt90) REVERT: C 281 GLU cc_start: 0.8044 (mp0) cc_final: 0.7786 (mp0) REVERT: C 962 ASP cc_start: 0.8073 (t0) cc_final: 0.7633 (t0) REVERT: C 1017 LEU cc_start: 0.9292 (mt) cc_final: 0.9047 (mt) REVERT: P 1 MET cc_start: 0.5479 (mtt) cc_final: 0.5236 (mtt) REVERT: P 36 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8778 (tm-30) REVERT: P 39 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8788 (tm-30) REVERT: Q 3 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7883 (mmm160) REVERT: Q 17 GLN cc_start: 0.9316 (mm110) cc_final: 0.9087 (mm-40) REVERT: Q 30 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8404 (tt) outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.3680 time to fit residues: 111.3255 Evaluate side-chains 185 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN C 881 ASN C 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22428 Z= 0.307 Angle : 0.508 10.083 30442 Z= 0.258 Chirality : 0.039 0.133 3342 Planarity : 0.004 0.059 4015 Dihedral : 3.669 37.802 3018 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.07 % Allowed : 10.28 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.16 (0.16), residues: 2736 helix: 2.51 (0.14), residues: 1472 sheet: 1.24 (0.34), residues: 225 loop : -0.09 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 265 HIS 0.003 0.001 HIS C 843 PHE 0.029 0.002 PHE B 293 TYR 0.024 0.001 TYR B1111 ARG 0.013 0.000 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8827 (pp) REVERT: B 541 MET cc_start: 0.8581 (mtp) cc_final: 0.8220 (mtp) REVERT: B 823 ARG cc_start: 0.7048 (ttm170) cc_final: 0.6458 (mmm-85) REVERT: B 902 ARG cc_start: 0.8536 (ptt180) cc_final: 0.8229 (ptt-90) REVERT: C 266 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7310 (ttt90) REVERT: C 281 GLU cc_start: 0.8060 (mp0) cc_final: 0.7797 (mp0) REVERT: C 962 ASP cc_start: 0.8189 (t0) cc_final: 0.7800 (t0) REVERT: C 1017 LEU cc_start: 0.9325 (mt) cc_final: 0.9084 (mt) REVERT: D 160 VAL cc_start: 0.8203 (t) cc_final: 0.7851 (p) REVERT: P 1 MET cc_start: 0.5662 (mtt) cc_final: 0.5411 (mtt) REVERT: P 39 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8802 (tm-30) REVERT: Q 3 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7809 (mmm160) REVERT: Q 17 GLN cc_start: 0.9326 (mm110) cc_final: 0.9082 (mm-40) outliers start: 25 outliers final: 18 residues processed: 189 average time/residue: 0.3472 time to fit residues: 103.1093 Evaluate side-chains 183 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 881 ASN C 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22428 Z= 0.179 Angle : 0.467 9.239 30442 Z= 0.235 Chirality : 0.037 0.139 3342 Planarity : 0.004 0.064 4015 Dihedral : 3.530 35.919 3018 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.81 % Allowed : 10.79 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.29 (0.16), residues: 2736 helix: 2.61 (0.14), residues: 1458 sheet: 1.36 (0.35), residues: 223 loop : 0.00 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 265 HIS 0.002 0.000 HIS C 185 PHE 0.023 0.001 PHE B 31 TYR 0.022 0.001 TYR B1111 ARG 0.014 0.000 ARG Q 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8837 (pp) REVERT: B 541 MET cc_start: 0.8526 (mtp) cc_final: 0.8187 (mtp) REVERT: B 823 ARG cc_start: 0.7000 (ttm170) cc_final: 0.6429 (mmm-85) REVERT: B 902 ARG cc_start: 0.8518 (ptt180) cc_final: 0.8215 (ptt-90) REVERT: C 266 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7311 (ttt90) REVERT: C 281 GLU cc_start: 0.8069 (mp0) cc_final: 0.7791 (mp0) REVERT: C 962 ASP cc_start: 0.8148 (t0) cc_final: 0.7754 (t0) REVERT: C 1017 LEU cc_start: 0.9281 (mt) cc_final: 0.9064 (mt) REVERT: D 160 VAL cc_start: 0.8028 (t) cc_final: 0.7805 (p) REVERT: P 39 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8716 (tm-30) REVERT: Q 3 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7790 (mmm160) outliers start: 19 outliers final: 16 residues processed: 183 average time/residue: 0.3772 time to fit residues: 106.6044 Evaluate side-chains 175 residues out of total 2345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 1084 ASN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 221 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 881 ASN C 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.063018 restraints weight = 42383.709| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.56 r_work: 0.2548 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22428 Z= 0.375 Angle : 0.549 9.608 30442 Z= 0.277 Chirality : 0.041 0.153 3342 Planarity : 0.004 0.047 4015 Dihedral : 3.780 38.322 3018 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.94 % Allowed : 10.70 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 2.00 (0.16), residues: 2736 helix: 2.37 (0.14), residues: 1478 sheet: 1.25 (0.34), residues: 231 loop : -0.20 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS B 440 PHE 0.027 0.002 PHE B 293 TYR 0.026 0.002 TYR B1111 ARG 0.010 0.000 ARG Q 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4344.92 seconds wall clock time: 78 minutes 47.42 seconds (4727.42 seconds total)