Starting phenix.real_space_refine (version: dev) on Fri Feb 24 23:58:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b1u_15805/02_2023/8b1u_15805_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" 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 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B ARG 824": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B ASP 899": "OD1" <-> "OD2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1059": "NH1" <-> "NH2" 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 "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" 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 TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 713": "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 ARG 804": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 858": "NH1" <-> "NH2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 935": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1068": "NH1" <-> "NH2" Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24127 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 9145 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 1 Chain: "C" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8738 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1014} Chain breaks: 1 Chain: "D" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4644 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 25, 'TRANS': 575} Chain breaks: 1 Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 533 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.72, per 1000 atoms: 0.53 Number of scatterers: 24127 At special positions: 0 Unit cell: (154.76, 152.64, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 53 15.00 Mg 1 11.99 O 4632 8.00 N 4249 7.00 C 15088 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: 10.13 Conformation dependent library (CDL) restraints added in 3.2 seconds 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 15 sheets defined 48.8% alpha, 8.1% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 8.88 Creating SS restraints... Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.722A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 66 through 89 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 123 removed outlier: 5.004A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 157 through 171 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.644A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.517A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 238 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 324 through 346 removed outlier: 3.859A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 366 through 377 removed outlier: 4.426A pdb=" N THR B 376 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 377 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 635 through 655 Processing helix chain 'B' and resid 658 through 668 Processing helix chain 'B' and resid 670 through 676 Processing helix chain 'B' and resid 680 through 700 removed outlier: 3.967A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 716 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 806 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 850 through 860 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 949 through 960 removed outlier: 3.543A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 Processing helix chain 'B' and resid 984 through 998 Proline residue: B 988 - end of helix removed outlier: 4.062A pdb=" N THR B 991 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1011 No H-bonds generated for 'chain 'B' and resid 1009 through 1011' Processing helix chain 'B' and resid 1033 through 1043 removed outlier: 4.659A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1049 Processing helix chain 'B' and resid 1090 through 1093 Processing helix chain 'B' and resid 1095 through 1105 Processing helix chain 'B' and resid 1107 through 1125 Processing helix chain 'B' and resid 1131 through 1134 No H-bonds generated for 'chain 'B' and resid 1131 through 1134' Processing helix chain 'B' and resid 1162 through 1173 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.737A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 122 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.595A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 4.613A pdb=" N ALA C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Proline residue: C 167 - end of helix removed outlier: 4.317A pdb=" N GLU C 174 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 removed outlier: 4.749A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.814A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.754A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 382 through 399 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 415 through 428 Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.838A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 524 through 536 Processing helix chain 'C' and resid 556 through 577 removed outlier: 3.837A pdb=" N ALA C 565 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 568 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET C 569 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP C 574 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 598 removed outlier: 3.505A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Proline residue: C 589 - end of helix removed outlier: 4.715A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.597A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 791 through 794 Processing helix chain 'C' and resid 807 through 810 No H-bonds generated for 'chain 'C' and resid 807 through 810' Processing helix chain 'C' and resid 834 through 842 Processing helix chain 'C' and resid 844 through 850 Processing helix chain 'C' and resid 875 through 889 Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 911 through 934 removed outlier: 3.743A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 990 Processing helix chain 'C' and resid 1013 through 1032 Processing helix chain 'C' and resid 1041 through 1049 Processing helix chain 'C' and resid 1061 through 1076 Processing helix chain 'C' and resid 1088 through 1093 removed outlier: 3.569A pdb=" N ARG C1092 " --> pdb=" O ILE C1088 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1088 through 1093' Processing helix chain 'C' and resid 1099 through 1119 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.732A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 33 through 47 Processing helix chain 'D' and resid 66 through 75 removed outlier: 4.911A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'D' and resid 110 through 124 removed outlier: 3.544A pdb=" N CYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 144 Processing helix chain 'D' and resid 153 through 163 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.625A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.505A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 319 removed outlier: 4.336A pdb=" N TYR D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 401 through 423 removed outlier: 4.831A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 437 removed outlier: 3.739A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.725A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.554A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.822A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 41 through 65 Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.500A pdb=" N LEU B 409 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 21 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 411 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 487 through 490 Processing sheet with id= C, first strand: chain 'B' and resid 865 through 870 removed outlier: 6.681A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS B 813 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TRP B 502 " --> pdb=" O CYS B 813 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 815 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET B 504 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL B 817 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN B 737 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 558 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 739 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 767 through 769 Processing sheet with id= E, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.375A pdb=" N ARG B1059 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 904 " --> pdb=" O ARG B1059 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET B1061 " --> pdb=" O THR B 904 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1017 through 1019 removed outlier: 3.655A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.526A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 236 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C 5 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 238 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER C 7 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 240 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET C 34 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N CYS C 214 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU C 36 " --> pdb=" O CYS C 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 365 through 367 Processing sheet with id= I, first strand: chain 'C' and resid 781 through 783 removed outlier: 8.623A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU C 727 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N HIS C 377 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 729 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS C 379 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 731 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN C 660 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 412 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS C 662 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.122A pdb=" N GLN C 951 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 963 through 968 removed outlier: 6.372A pdb=" N GLU C 995 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG C 966 " --> pdb=" O GLU C 995 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG C 997 " --> pdb=" O ARG C 966 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG C 968 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 999 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 100 through 103 Processing sheet with id= M, first strand: chain 'D' and resid 352 through 355 removed outlier: 8.481A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 292 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 169 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE D 294 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY D 171 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY D 296 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.744A pdb=" N LEU D 577 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG D 396 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU D 579 " --> pdb=" O ARG D 396 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 530 through 532 removed outlier: 7.142A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 9.69 Time building geometry restraints manager: 10.82 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: 7168 1.34 - 1.45: 3901 1.45 - 1.57: 13403 1.57 - 1.69: 104 1.69 - 1.81: 174 Bond restraints: 24750 Sorted by residual: bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O3G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O2B ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 24745 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 860 105.88 - 112.91: 13167 112.91 - 119.94: 8025 119.94 - 126.97: 11298 126.97 - 134.00: 445 Bond angle restraints: 33795 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " pdb=" O2B ANP B1501 " ideal model delta sigma weight residual 120.08 109.49 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LEU C 323 " pdb=" CB LEU C 323 " pdb=" CG LEU C 323 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.53e+00 angle pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " pdb=" O2G ANP B1501 " ideal model delta sigma weight residual 101.05 109.44 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C PRO B 174 " pdb=" N LEU B 175 " pdb=" CA LEU B 175 " ideal model delta sigma weight residual 120.51 124.40 -3.89 1.45e+00 4.76e-01 7.18e+00 ... (remaining 33790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13877 17.67 - 35.35: 587 35.35 - 53.02: 223 53.02 - 70.70: 77 70.70 - 88.37: 5 Dihedral angle restraints: 14769 sinusoidal: 6367 harmonic: 8402 Sorted by residual: dihedral pdb=" CA ASN B1003 " pdb=" C ASN B1003 " pdb=" N GLU B1004 " pdb=" CA GLU B1004 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+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 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP C 484 " pdb=" CB ASP C 484 " pdb=" CG ASP C 484 " pdb=" OD1 ASP C 484 " ideal model delta sinusoidal sigma weight residual -30.00 -85.10 55.10 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 14766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3253 0.052 - 0.104: 394 0.104 - 0.155: 61 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 3710 Sorted by residual: chirality pdb=" C3' ANP B1501 " pdb=" C2' ANP B1501 " pdb=" C4' ANP B1501 " pdb=" O3' ANP B1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU C 323 " pdb=" CB LEU C 323 " pdb=" CD1 LEU C 323 " pdb=" CD2 LEU C 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 3707 not shown) Planarity restraints: 4257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO C 658 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 50 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 51 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 382 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.019 5.00e-02 4.00e+02 ... (remaining 4254 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 713 2.72 - 3.26: 23834 3.26 - 3.81: 38726 3.81 - 4.35: 47676 4.35 - 4.90: 79932 Nonbonded interactions: 190881 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.172 2.170 nonbonded pdb=" O2G ANP B1501 " pdb="MG MG B1502 " model vdw 2.202 2.170 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.215 2.440 nonbonded pdb=" O ASN B 889 " pdb=" NE2 GLN C 800 " model vdw 2.237 2.520 nonbonded pdb=" O ALA B 361 " pdb=" OG SER B 364 " model vdw 2.250 2.440 ... (remaining 190876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 53 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 15088 2.51 5 N 4249 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 4.940 Check model and map are aligned: 0.340 Process input model: 67.110 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.002 0.143 24750 Z= 0.151 Angle : 0.512 17.029 33795 Z= 0.307 Chirality : 0.035 0.259 3710 Planarity : 0.003 0.053 4257 Dihedral : 12.034 88.373 9323 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.66 (0.14), residues: 2872 helix: 0.05 (0.12), residues: 1493 sheet: -0.51 (0.27), residues: 296 loop : -0.94 (0.17), residues: 1083 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 652 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 4 residues processed: 676 average time/residue: 0.4366 time to fit residues: 436.3153 Evaluate side-chains 255 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2482 time to fit residues: 5.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 181 GLN B 291 GLN B 458 ASN B 484 ASN B 624 ASN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN B1072 HIS B1103 GLN B1134 HIS B1161 ASN C 137 GLN C 185 HIS C 336 HIS C 390 HIS C 448 HIS C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 50 HIS D 247 GLN D 256 HIS D 464 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 24750 Z= 0.274 Angle : 0.574 9.300 33795 Z= 0.291 Chirality : 0.040 0.230 3710 Planarity : 0.004 0.063 4257 Dihedral : 13.269 89.448 3686 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.49 (0.15), residues: 2872 helix: 1.09 (0.13), residues: 1472 sheet: -0.15 (0.27), residues: 305 loop : -0.48 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 32 residues processed: 300 average time/residue: 0.3716 time to fit residues: 176.7782 Evaluate side-chains 223 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2612 time to fit residues: 18.9379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 213 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 202 GLN B 403 HIS B 484 ASN B 705 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN C 87 ASN C 191 GLN C 448 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 24750 Z= 0.317 Angle : 0.588 8.437 33795 Z= 0.301 Chirality : 0.040 0.152 3710 Planarity : 0.004 0.046 4257 Dihedral : 13.387 82.123 3686 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.70 (0.15), residues: 2872 helix: 1.23 (0.13), residues: 1479 sheet: 0.12 (0.28), residues: 304 loop : -0.39 (0.18), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 223 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 265 average time/residue: 0.3359 time to fit residues: 145.6275 Evaluate side-chains 210 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2162 time to fit residues: 12.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 127 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 24750 Z= 0.319 Angle : 0.588 8.772 33795 Z= 0.301 Chirality : 0.040 0.270 3710 Planarity : 0.004 0.044 4257 Dihedral : 13.480 87.742 3686 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.70 (0.15), residues: 2872 helix: 1.24 (0.13), residues: 1467 sheet: 0.24 (0.28), residues: 303 loop : -0.43 (0.18), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 202 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 244 average time/residue: 0.3433 time to fit residues: 138.5179 Evaluate side-chains 196 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2142 time to fit residues: 12.0502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 24750 Z= 0.332 Angle : 0.595 10.498 33795 Z= 0.300 Chirality : 0.040 0.163 3710 Planarity : 0.004 0.044 4257 Dihedral : 13.451 87.319 3686 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.69 (0.16), residues: 2872 helix: 1.24 (0.14), residues: 1458 sheet: 0.29 (0.29), residues: 296 loop : -0.45 (0.18), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 223 average time/residue: 0.3666 time to fit residues: 135.2094 Evaluate side-chains 190 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2231 time to fit residues: 9.7280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 20.0000 chunk 255 optimal weight: 0.0060 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 283 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 chunk 148 optimal weight: 0.8980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 594 GLN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 24750 Z= 0.166 Angle : 0.510 9.501 33795 Z= 0.255 Chirality : 0.037 0.172 3710 Planarity : 0.003 0.050 4257 Dihedral : 13.282 89.257 3686 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.97 (0.16), residues: 2872 helix: 1.51 (0.14), residues: 1472 sheet: 0.54 (0.29), residues: 298 loop : -0.46 (0.18), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 227 average time/residue: 0.3467 time to fit residues: 128.7399 Evaluate side-chains 189 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 2.853 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2343 time to fit residues: 8.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 321 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 24750 Z= 0.262 Angle : 0.557 9.954 33795 Z= 0.278 Chirality : 0.038 0.186 3710 Planarity : 0.004 0.049 4257 Dihedral : 13.307 89.685 3686 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.98 (0.16), residues: 2872 helix: 1.52 (0.14), residues: 1456 sheet: 0.50 (0.29), residues: 298 loop : -0.40 (0.18), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 204 average time/residue: 0.3583 time to fit residues: 122.0605 Evaluate side-chains 183 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2366 time to fit residues: 8.0786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 168 optimal weight: 0.0070 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 24750 Z= 0.309 Angle : 0.588 10.764 33795 Z= 0.294 Chirality : 0.039 0.153 3710 Planarity : 0.004 0.069 4257 Dihedral : 13.383 89.635 3686 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.81 (0.16), residues: 2872 helix: 1.37 (0.14), residues: 1454 sheet: 0.38 (0.29), residues: 286 loop : -0.44 (0.18), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 206 average time/residue: 0.3564 time to fit residues: 120.8818 Evaluate side-chains 183 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2256 time to fit residues: 6.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 20.0000 chunk 270 optimal weight: 0.0000 chunk 246 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 473 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 24750 Z= 0.371 Angle : 0.642 11.925 33795 Z= 0.321 Chirality : 0.040 0.172 3710 Planarity : 0.004 0.053 4257 Dihedral : 13.511 89.914 3686 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.54 (0.16), residues: 2872 helix: 1.15 (0.14), residues: 1464 sheet: 0.17 (0.30), residues: 281 loop : -0.56 (0.18), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 193 average time/residue: 0.3552 time to fit residues: 113.6901 Evaluate side-chains 176 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 2.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2197 time to fit residues: 4.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 24750 Z= 0.370 Angle : 0.651 12.313 33795 Z= 0.325 Chirality : 0.041 0.195 3710 Planarity : 0.005 0.076 4257 Dihedral : 13.550 88.038 3686 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.44 (0.16), residues: 2872 helix: 1.09 (0.14), residues: 1455 sheet: 0.06 (0.30), residues: 280 loop : -0.62 (0.18), residues: 1137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 186 average time/residue: 0.3594 time to fit residues: 111.2890 Evaluate side-chains 180 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2242 time to fit residues: 6.3634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.5980 chunk 247 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 29 optimal weight: 0.0980 chunk 42 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 GLN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.078612 restraints weight = 61594.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080616 restraints weight = 35339.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081955 restraints weight = 22508.724| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24750 Z= 0.170 Angle : 0.559 11.939 33795 Z= 0.275 Chirality : 0.038 0.227 3710 Planarity : 0.004 0.050 4257 Dihedral : 13.310 86.592 3686 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.87 (0.16), residues: 2872 helix: 1.49 (0.14), residues: 1445 sheet: 0.29 (0.31), residues: 280 loop : -0.47 (0.18), residues: 1147 =============================================================================== Job complete usr+sys time: 3930.96 seconds wall clock time: 74 minutes 35.69 seconds (4475.69 seconds total)