Starting phenix.real_space_refine on Sun Mar 17 04:26:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr2_23954/03_2024/7mr2_23954.pdb" } resolution = 4.3 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= 0.003 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10553 2.51 5 N 2927 2.21 5 O 3111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1061": "OD1" <-> "OD2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16671 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 6827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6827 Classifications: {'peptide': 855} Link IDs: {'PTRANS': 34, 'TRANS': 820} Chain breaks: 1 Chain: "C" Number of atoms: 8887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8887 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1032} Chain breaks: 1 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Time building chain proxies: 8.80, per 1000 atoms: 0.53 Number of scatterers: 16671 At special positions: 0 Unit cell: (141.25, 128.82, 142.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3111 8.00 N 2927 7.00 C 10553 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: 6.32 Conformation dependent library (CDL) restraints added in 2.9 seconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 55.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.813A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 67 through 90 removed outlier: 3.677A pdb=" N GLU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.886A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.798A pdb=" N GLU B 123 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.507A pdb=" N ASN B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.110A pdb=" N LEU B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.221A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 217 through 235 removed outlier: 3.972A pdb=" N THR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.917A pdb=" N ALA B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.654A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.931A pdb=" N LEU B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 287 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.642A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.329A pdb=" N THR B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.549A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.528A pdb=" N ALA B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 420 through 424 removed outlier: 4.041A pdb=" N GLY B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.813A pdb=" N MET B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.586A pdb=" N PHE B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 534 removed outlier: 3.650A pdb=" N MET B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.747A pdb=" N VAL B 567 " --> pdb=" O GLU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.084A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.579A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.532A pdb=" N ASN B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.567A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 645 " --> pdb=" O VAL B 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 650 " --> pdb=" O ASP B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.511A pdb=" N LEU B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 669 " --> pdb=" O MET B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.691A pdb=" N ASP B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 687 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 688 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 695 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 716 removed outlier: 3.568A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 712 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.705A pdb=" N GLN B 725 " --> pdb=" O ALA B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 806 Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 844 removed outlier: 3.950A pdb=" N ARG B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 842 " --> pdb=" O LEU B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 4.116A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.199A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.748A 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 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.148A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.711A 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 Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.117A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.533A pdb=" N LEU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.545A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.652A pdb=" N LEU C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 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 418 through 428 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.800A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (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 558 through 578 removed outlier: 3.971A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 633 through 646 removed outlier: 4.278A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.655A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 757 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.143A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 4.047A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 889 removed outlier: 3.704A pdb=" N ALA C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 911 through 933 removed outlier: 4.257A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.780A pdb=" N LEU C 980 " --> pdb=" O GLN C 976 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1003 No H-bonds generated for 'chain 'C' and resid 1001 through 1003' Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.545A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1049 removed outlier: 4.093A pdb=" N THR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1076 removed outlier: 3.982A pdb=" N LYS C1066 " --> pdb=" O SER C1062 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 4.032A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1114 through 1120 removed outlier: 3.731A pdb=" N ARG C1118 " --> pdb=" O LEU C1114 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.652A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 110 through 124 Processing sheet with id=AA1, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.516A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 441 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.526A 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 209 removed outlier: 6.188A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 489 removed outlier: 3.583A pdb=" N MET B 541 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.058A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N CYS B 813 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 752 " --> pdb=" O CYS B 813 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.688A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 264 through 265 Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.199A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 4.011A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 662 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS C 673 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 675 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 730 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 729 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 731 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.198A pdb=" N VAL C 832 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N TRP C 955 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 965 through 967 removed outlier: 6.787A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 998 " --> pdb=" O TRP C1006 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.877A pdb=" N ASP C1051 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.809A pdb=" N LEU D 102 " --> pdb=" O SER D 92 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2163 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: 5.32 Time building geometry restraints manager: 6.81 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: 5573 1.34 - 1.46: 3311 1.46 - 1.58: 8023 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 17039 Sorted by residual: bond pdb=" CA ASN D 80 " pdb=" CB ASN D 80 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.37e-02 5.33e+03 2.85e+00 bond pdb=" CG1 ILE B 865 " pdb=" CD1 ILE B 865 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CB LYS B 268 " pdb=" CG LYS B 268 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C SER C 419 " pdb=" N PRO C 420 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.62e+00 bond pdb=" CA ASN D 80 " pdb=" C ASN D 80 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.35e-02 5.49e+03 1.48e+00 ... (remaining 17034 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.09: 449 106.09 - 113.17: 8971 113.17 - 120.25: 6512 120.25 - 127.32: 6978 127.32 - 134.40: 213 Bond angle restraints: 23123 Sorted by residual: angle pdb=" C ASN D 80 " pdb=" CA ASN D 80 " pdb=" CB ASN D 80 " ideal model delta sigma weight residual 111.41 119.87 -8.46 1.65e+00 3.67e-01 2.63e+01 angle pdb=" C PHE C 483 " pdb=" N ASP C 484 " pdb=" CA ASP C 484 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" CB MET B 499 " pdb=" CG MET B 499 " pdb=" SD MET B 499 " ideal model delta sigma weight residual 112.70 124.71 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB LYS B 268 " pdb=" CG LYS B 268 " pdb=" CD LYS B 268 " ideal model delta sigma weight residual 111.30 120.22 -8.92 2.30e+00 1.89e-01 1.50e+01 angle pdb=" N MET C 569 " pdb=" CA MET C 569 " pdb=" CB MET C 569 " ideal model delta sigma weight residual 110.28 115.90 -5.62 1.55e+00 4.16e-01 1.32e+01 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 9139 17.44 - 34.89: 965 34.89 - 52.33: 152 52.33 - 69.78: 40 69.78 - 87.22: 26 Dihedral angle restraints: 10322 sinusoidal: 4262 harmonic: 6060 Sorted by residual: dihedral pdb=" CA LEU C 460 " pdb=" C LEU C 460 " pdb=" N PRO C 461 " pdb=" CA PRO C 461 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER C 268 " pdb=" C SER C 268 " pdb=" N PHE C 269 " pdb=" CA PHE C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASP B 862 " pdb=" C ASP B 862 " pdb=" N ASP B 863 " pdb=" CA ASP B 863 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 10319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2237 0.073 - 0.146: 284 0.146 - 0.218: 11 0.218 - 0.291: 1 0.291 - 0.364: 1 Chirality restraints: 2534 Sorted by residual: chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB THR C 402 " pdb=" CA THR C 402 " pdb=" OG1 THR C 402 " pdb=" CG2 THR C 402 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASP C 484 " pdb=" N ASP C 484 " pdb=" C ASP C 484 " pdb=" CB ASP C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2531 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C1114 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO C1115 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C1115 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C1115 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 582 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO C 583 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 583 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 583 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO C 658 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.041 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3687 2.79 - 3.31: 15624 3.31 - 3.84: 27053 3.84 - 4.37: 29040 4.37 - 4.90: 49456 Nonbonded interactions: 124860 Sorted by model distance: nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLN B 765 " model vdw 2.290 2.440 nonbonded pdb=" O VAL B 804 " pdb=" NH2 ARG B 808 " model vdw 2.310 2.520 nonbonded pdb=" O SER B 720 " pdb=" OG SER B 720 " model vdw 2.318 2.440 nonbonded pdb=" OE2 GLU C 357 " pdb=" ND2 ASN C 363 " model vdw 2.322 2.520 ... (remaining 124855 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 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 44.150 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.003 0.061 17039 Z= 0.208 Angle : 0.752 12.011 23123 Z= 0.381 Chirality : 0.046 0.364 2534 Planarity : 0.006 0.083 3042 Dihedral : 14.956 87.219 6382 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.32 (0.18), residues: 2065 helix: -0.12 (0.15), residues: 1037 sheet: -1.37 (0.42), residues: 161 loop : -1.63 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 544 HIS 0.003 0.001 HIS B 705 PHE 0.030 0.002 PHE D 23 TYR 0.010 0.001 TYR B 394 ARG 0.009 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: B 620 MET cc_start: 0.8736 (tpp) cc_final: 0.8493 (tpp) REVERT: C 537 MET cc_start: 0.8330 (ppp) cc_final: 0.8009 (ppp) REVERT: C 1080 MET cc_start: 0.8847 (ppp) cc_final: 0.8542 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2458 time to fit residues: 35.4934 Evaluate side-chains 72 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 181 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17039 Z= 0.275 Angle : 0.589 7.246 23123 Z= 0.304 Chirality : 0.040 0.161 2534 Planarity : 0.005 0.072 3042 Dihedral : 4.666 21.621 2280 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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 (0.19), residues: 2065 helix: 0.63 (0.16), residues: 1039 sheet: -1.72 (0.40), residues: 159 loop : -1.48 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 811 HIS 0.004 0.001 HIS B 769 PHE 0.015 0.001 PHE C 789 TYR 0.015 0.002 TYR B 394 ARG 0.003 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9201 (ttm) cc_final: 0.8968 (ttm) REVERT: B 620 MET cc_start: 0.9097 (tpp) cc_final: 0.8821 (tpp) REVERT: C 287 PHE cc_start: 0.8364 (t80) cc_final: 0.8120 (t80) REVERT: C 537 MET cc_start: 0.8065 (ppp) cc_final: 0.7620 (ppp) REVERT: C 941 MET cc_start: 0.9014 (tmm) cc_final: 0.8730 (tmm) REVERT: C 1080 MET cc_start: 0.8883 (ppp) cc_final: 0.8512 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2514 time to fit residues: 34.1605 Evaluate side-chains 69 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 155 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17039 Z= 0.196 Angle : 0.526 5.849 23123 Z= 0.270 Chirality : 0.040 0.146 2534 Planarity : 0.004 0.078 3042 Dihedral : 4.483 20.881 2280 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.31 (0.19), residues: 2065 helix: 0.93 (0.16), residues: 1036 sheet: -1.64 (0.40), residues: 157 loop : -1.29 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 811 HIS 0.002 0.001 HIS C 377 PHE 0.016 0.001 PHE C 789 TYR 0.013 0.001 TYR B 394 ARG 0.002 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9139 (ttm) cc_final: 0.8835 (ttp) REVERT: B 620 MET cc_start: 0.9108 (tpp) cc_final: 0.8890 (tpp) REVERT: B 648 TYR cc_start: 0.8434 (m-10) cc_final: 0.8049 (m-80) REVERT: C 287 PHE cc_start: 0.8324 (t80) cc_final: 0.8085 (t80) REVERT: C 537 MET cc_start: 0.8189 (ppp) cc_final: 0.7700 (ppp) REVERT: C 941 MET cc_start: 0.9013 (tmm) cc_final: 0.8730 (tmm) REVERT: C 1080 MET cc_start: 0.8857 (ppp) cc_final: 0.8479 (ppp) REVERT: D 107 LEU cc_start: 0.9000 (tp) cc_final: 0.8794 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2456 time to fit residues: 35.1924 Evaluate side-chains 71 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17039 Z= 0.157 Angle : 0.500 6.508 23123 Z= 0.255 Chirality : 0.039 0.155 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.308 22.119 2280 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.12 (0.19), residues: 2065 helix: 1.10 (0.16), residues: 1043 sheet: -1.41 (0.41), residues: 153 loop : -1.28 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 587 HIS 0.003 0.001 HIS B 171 PHE 0.027 0.001 PHE C 135 TYR 0.014 0.001 TYR D 108 ARG 0.002 0.000 ARG B 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.088 Fit side-chains revert: symmetry clash REVERT: B 354 MET cc_start: 0.9135 (ttm) cc_final: 0.8838 (ttp) REVERT: B 648 TYR cc_start: 0.8371 (m-10) cc_final: 0.7966 (m-80) REVERT: C 287 PHE cc_start: 0.8325 (t80) cc_final: 0.8059 (t80) REVERT: C 537 MET cc_start: 0.8190 (ppp) cc_final: 0.7695 (ppp) REVERT: C 941 MET cc_start: 0.8947 (tmm) cc_final: 0.8681 (tmm) REVERT: C 1080 MET cc_start: 0.8861 (ppp) cc_final: 0.8450 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2615 time to fit residues: 39.6844 Evaluate side-chains 70 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS B 737 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17039 Z= 0.166 Angle : 0.508 6.717 23123 Z= 0.257 Chirality : 0.039 0.154 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.224 21.838 2280 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.01 (0.19), residues: 2065 helix: 1.20 (0.16), residues: 1037 sheet: -1.37 (0.41), residues: 153 loop : -1.22 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 710 HIS 0.002 0.001 HIS B 705 PHE 0.017 0.001 PHE C 901 TYR 0.011 0.001 TYR B 394 ARG 0.001 0.000 ARG B 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9105 (ttm) cc_final: 0.8765 (ttp) REVERT: B 620 MET cc_start: 0.9105 (tpp) cc_final: 0.8879 (tpp) REVERT: B 648 TYR cc_start: 0.8387 (m-10) cc_final: 0.7960 (m-80) REVERT: C 287 PHE cc_start: 0.8266 (t80) cc_final: 0.7970 (t80) REVERT: C 396 MET cc_start: 0.8930 (tmm) cc_final: 0.8647 (tmm) REVERT: C 537 MET cc_start: 0.8180 (ppp) cc_final: 0.7647 (ppp) REVERT: C 1080 MET cc_start: 0.8900 (ppp) cc_final: 0.8506 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2709 time to fit residues: 40.5391 Evaluate side-chains 70 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17039 Z= 0.247 Angle : 0.565 7.082 23123 Z= 0.285 Chirality : 0.040 0.158 2534 Planarity : 0.004 0.077 3042 Dihedral : 4.376 21.340 2280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.11 (0.19), residues: 2065 helix: 1.12 (0.16), residues: 1037 sheet: -1.44 (0.41), residues: 152 loop : -1.26 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 710 HIS 0.003 0.001 HIS C 267 PHE 0.014 0.001 PHE C 789 TYR 0.020 0.001 TYR C 310 ARG 0.008 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8639 (tpp) cc_final: 0.8392 (tpp) REVERT: B 354 MET cc_start: 0.9162 (ttm) cc_final: 0.8808 (ttp) REVERT: B 499 MET cc_start: 0.8521 (tpt) cc_final: 0.8292 (tpt) REVERT: B 518 MET cc_start: 0.8227 (mtp) cc_final: 0.7779 (mtp) REVERT: B 620 MET cc_start: 0.9223 (tpp) cc_final: 0.8966 (tpp) REVERT: C 396 MET cc_start: 0.8968 (tmm) cc_final: 0.8673 (tmm) REVERT: C 537 MET cc_start: 0.8120 (ppp) cc_final: 0.7726 (ppp) REVERT: C 1031 MET cc_start: 0.8663 (tpp) cc_final: 0.8301 (tpp) REVERT: C 1080 MET cc_start: 0.8852 (ppp) cc_final: 0.8433 (ppp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2407 time to fit residues: 34.5087 Evaluate side-chains 68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 112 optimal weight: 0.0870 chunk 167 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17039 Z= 0.184 Angle : 0.530 7.524 23123 Z= 0.268 Chirality : 0.040 0.153 2534 Planarity : 0.004 0.076 3042 Dihedral : 4.260 20.868 2280 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.01 (0.19), residues: 2065 helix: 1.21 (0.16), residues: 1039 sheet: -1.37 (0.42), residues: 153 loop : -1.21 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 710 HIS 0.003 0.001 HIS B 812 PHE 0.015 0.001 PHE C 789 TYR 0.019 0.001 TYR C 310 ARG 0.003 0.000 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8564 (tpp) cc_final: 0.8342 (tpp) REVERT: B 354 MET cc_start: 0.9138 (ttm) cc_final: 0.8765 (ttp) REVERT: C 396 MET cc_start: 0.8904 (tmm) cc_final: 0.8585 (tmm) REVERT: C 531 MET cc_start: 0.8669 (tpp) cc_final: 0.8260 (tpp) REVERT: C 537 MET cc_start: 0.8126 (ppp) cc_final: 0.7706 (ppp) REVERT: C 1031 MET cc_start: 0.8661 (tpp) cc_final: 0.8278 (tpp) REVERT: C 1080 MET cc_start: 0.8858 (ppp) cc_final: 0.8424 (ppp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2415 time to fit residues: 34.9553 Evaluate side-chains 67 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 0.0000 chunk 156 optimal weight: 9.9990 overall best weight: 2.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17039 Z= 0.189 Angle : 0.538 12.486 23123 Z= 0.270 Chirality : 0.040 0.156 2534 Planarity : 0.004 0.075 3042 Dihedral : 4.231 20.476 2280 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.04 (0.19), residues: 2065 helix: 1.23 (0.16), residues: 1047 sheet: -1.31 (0.42), residues: 153 loop : -1.22 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 710 HIS 0.004 0.001 HIS C 390 PHE 0.015 0.001 PHE C 789 TYR 0.017 0.001 TYR C 310 ARG 0.003 0.000 ARG C 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8604 (tpp) cc_final: 0.8379 (tpp) REVERT: B 354 MET cc_start: 0.9136 (ttm) cc_final: 0.8828 (ttm) REVERT: B 620 MET cc_start: 0.9145 (tpp) cc_final: 0.8893 (tpp) REVERT: C 396 MET cc_start: 0.8851 (tmm) cc_final: 0.8615 (tmm) REVERT: C 531 MET cc_start: 0.8659 (tpp) cc_final: 0.8224 (tpp) REVERT: C 537 MET cc_start: 0.8125 (ppp) cc_final: 0.7708 (ppp) REVERT: C 1031 MET cc_start: 0.8658 (tpp) cc_final: 0.8247 (tpp) REVERT: C 1080 MET cc_start: 0.8864 (ppp) cc_final: 0.8435 (ppp) REVERT: D 30 ASP cc_start: 0.9089 (p0) cc_final: 0.8882 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2360 time to fit residues: 33.2930 Evaluate side-chains 70 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 173 optimal weight: 0.0980 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17039 Z= 0.299 Angle : 0.632 11.901 23123 Z= 0.316 Chirality : 0.041 0.156 2534 Planarity : 0.004 0.074 3042 Dihedral : 4.517 21.751 2280 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.06 % Allowed : 0.73 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.17 (0.19), residues: 2065 helix: 1.07 (0.16), residues: 1037 sheet: -1.42 (0.42), residues: 152 loop : -1.30 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 529 HIS 0.005 0.001 HIS B 812 PHE 0.014 0.001 PHE C 789 TYR 0.021 0.002 TYR C 310 ARG 0.003 0.000 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: B 121 MET cc_start: 0.8688 (tpp) cc_final: 0.8487 (tpp) REVERT: B 354 MET cc_start: 0.9169 (ttm) cc_final: 0.8847 (ttm) REVERT: B 518 MET cc_start: 0.8233 (mtp) cc_final: 0.7664 (mtp) REVERT: B 620 MET cc_start: 0.9189 (tpp) cc_final: 0.8988 (tpp) REVERT: B 863 ASP cc_start: 0.7920 (m-30) cc_final: 0.7530 (t0) REVERT: C 396 MET cc_start: 0.8961 (tmm) cc_final: 0.8710 (tmm) REVERT: C 537 MET cc_start: 0.8176 (ppp) cc_final: 0.7699 (ppp) REVERT: C 1031 MET cc_start: 0.8681 (tpp) cc_final: 0.8317 (tpp) REVERT: C 1080 MET cc_start: 0.8861 (ppp) cc_final: 0.8440 (ppp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2454 time to fit residues: 33.7601 Evaluate side-chains 68 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 0.0020 chunk 195 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17039 Z= 0.196 Angle : 0.559 11.210 23123 Z= 0.281 Chirality : 0.040 0.155 2534 Planarity : 0.004 0.074 3042 Dihedral : 4.376 21.128 2280 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.02 (0.19), residues: 2065 helix: 1.17 (0.16), residues: 1046 sheet: -1.35 (0.42), residues: 153 loop : -1.22 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 598 HIS 0.003 0.001 HIS C 377 PHE 0.016 0.001 PHE C 789 TYR 0.016 0.001 TYR C 310 ARG 0.003 0.000 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9137 (ttm) cc_final: 0.8804 (ttm) REVERT: B 518 MET cc_start: 0.8210 (mtp) cc_final: 0.7791 (mtp) REVERT: B 620 MET cc_start: 0.9156 (tpp) cc_final: 0.8882 (tpp) REVERT: B 863 ASP cc_start: 0.7845 (m-30) cc_final: 0.7507 (t0) REVERT: C 396 MET cc_start: 0.8936 (tmm) cc_final: 0.8688 (tmm) REVERT: C 537 MET cc_start: 0.8150 (ppp) cc_final: 0.7682 (ppp) REVERT: C 1031 MET cc_start: 0.8700 (tpp) cc_final: 0.8261 (tpp) REVERT: C 1080 MET cc_start: 0.8850 (ppp) cc_final: 0.8447 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2342 time to fit residues: 33.1521 Evaluate side-chains 69 residues out of total 1784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 150 optimal weight: 0.0470 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.050199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039554 restraints weight = 128132.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040588 restraints weight = 77475.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041260 restraints weight = 54888.344| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17039 Z= 0.130 Angle : 0.522 10.121 23123 Z= 0.259 Chirality : 0.039 0.155 2534 Planarity : 0.004 0.075 3042 Dihedral : 4.124 20.446 2280 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.24 (0.19), residues: 2065 helix: 1.39 (0.16), residues: 1048 sheet: -1.16 (0.43), residues: 153 loop : -1.13 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.004 0.001 HIS C 390 PHE 0.009 0.001 PHE C 287 TYR 0.012 0.001 TYR C 310 ARG 0.003 0.000 ARG C 786 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.58 seconds wall clock time: 43 minutes 18.93 seconds (2598.93 seconds total)