Starting phenix.real_space_refine on Mon Aug 5 09:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/08_2024/7n3n_24141.cif" } resolution = 3.33 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 82 5.16 5 Cl 2 4.86 5 C 8495 2.51 5 N 2140 2.21 5 O 2307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B GLU 1099": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B GLU 1106": "OE1" <-> "OE2" Residue "B GLU 1140": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6487 Classifications: {'peptide': 832} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 802} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 6497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6497 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 801} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.77, per 1000 atoms: 0.60 Number of scatterers: 13026 At special positions: 0 Unit cell: (81.32, 155.15, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 82 16.00 O 2307 8.00 N 2140 7.00 C 8495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 4 sheets defined 62.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.372A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.502A pdb=" N SER A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.067A pdb=" N LEU A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 399 removed outlier: 4.354A pdb=" N GLY A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 428 through 453 removed outlier: 4.405A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 removed outlier: 4.084A pdb=" N PHE A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.768A pdb=" N VAL A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.531A pdb=" N THR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.930A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 542 Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 599 through 633 removed outlier: 3.609A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 642 removed outlier: 5.454A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 667 Processing helix chain 'A' and resid 673 through 700 removed outlier: 4.192A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.736A pdb=" N SER A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 removed outlier: 3.542A pdb=" N TYR A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 801 through 813 removed outlier: 3.790A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.678A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix removed outlier: 3.609A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1097 through 1109 removed outlier: 3.792A pdb=" N ILE A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1130 removed outlier: 3.622A pdb=" N GLU A1130 " --> pdb=" O MET A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.941A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 removed outlier: 3.650A pdb=" N LEU B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 305 through 315 removed outlier: 4.436A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.806A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.626A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 3.671A pdb=" N ALA B 434 " --> pdb=" O TRP B 430 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 4.193A pdb=" N GLU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.507A pdb=" N VAL B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.405A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 544 removed outlier: 3.625A pdb=" N LYS B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 removed outlier: 3.553A pdb=" N CYS B 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 599 through 632 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 636 through 642 removed outlier: 4.474A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.928A pdb=" N LEU B 663 " --> pdb=" O PHE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 699 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 731 removed outlier: 3.658A pdb=" N ILE B 730 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 731 " --> pdb=" O MET B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 751 removed outlier: 3.538A pdb=" N ALA B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 779 removed outlier: 4.164A pdb=" N ASN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.858A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 849 Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.849A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1079 removed outlier: 3.962A pdb=" N ASP B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1119 through 1130 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 removed outlier: 3.588A pdb=" N SER B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.691A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 792 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 887 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET A 794 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 884 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 920 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 886 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A1197 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1165 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A1054 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N MET A1087 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1112 through 1113 Processing sheet with id=AA3, first strand: chain 'B' and resid 856 through 859 removed outlier: 7.717A pdb=" N ALA B 856 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 820 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 858 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N HIS B 822 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY B 887 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B1055 " --> pdb=" O ILE B1024 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1113 744 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2136 1.32 - 1.45: 3490 1.45 - 1.57: 7550 1.57 - 1.69: 0 1.69 - 1.82: 142 Bond restraints: 13318 Sorted by residual: bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CA ASN A 814 " pdb=" C ASN A 814 " ideal model delta sigma weight residual 1.526 1.463 0.062 1.31e-02 5.83e+03 2.26e+01 bond pdb=" CA LYS A 813 " pdb=" C LYS A 813 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.360 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 13313 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.96: 263 105.96 - 113.00: 7282 113.00 - 120.05: 4633 120.05 - 127.09: 5739 127.09 - 134.14: 148 Bond angle restraints: 18065 Sorted by residual: angle pdb=" N ARG A 482 " pdb=" CA ARG A 482 " pdb=" C ARG A 482 " ideal model delta sigma weight residual 111.28 121.00 -9.72 1.09e+00 8.42e-01 7.95e+01 angle pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" C PHE A 481 " ideal model delta sigma weight residual 110.80 123.72 -12.92 2.13e+00 2.20e-01 3.68e+01 angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.12 18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.37 17.80 3.00e+00 1.11e-01 3.52e+01 angle pdb=" N PRO A 479 " pdb=" CA PRO A 479 " pdb=" C PRO A 479 " ideal model delta sigma weight residual 113.53 119.48 -5.95 1.39e+00 5.18e-01 1.83e+01 ... (remaining 18060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7143 17.71 - 35.41: 591 35.41 - 53.12: 99 53.12 - 70.83: 24 70.83 - 88.53: 7 Dihedral angle restraints: 7864 sinusoidal: 3071 harmonic: 4793 Sorted by residual: dihedral pdb=" C PHE A 481 " pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual -122.60 -142.17 19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.90e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual -86.00 -146.43 60.43 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2070 0.187 - 0.373: 9 0.373 - 0.560: 2 0.560 - 0.747: 0 0.747 - 0.933: 1 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA PHE A 481 " pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CB PHE A 481 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE A 811 " pdb=" N PHE A 811 " pdb=" C PHE A 811 " pdb=" CB PHE A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ARG A 482 " pdb=" N ARG A 482 " pdb=" C ARG A 482 " pdb=" CB ARG A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 2079 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 300 " -0.023 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP A 300 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 300 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 300 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 300 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 300 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 300 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 300 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 728 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE B 728 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 728 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 728 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 728 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 728 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.35e+00 pdb=" CG PHE A 728 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 728 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 728 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 728 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 728 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 728 " -0.016 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 21 2.39 - 3.01: 7338 3.01 - 3.64: 20390 3.64 - 4.27: 29311 4.27 - 4.90: 49204 Nonbonded interactions: 106264 Sorted by model distance: nonbonded pdb=" CB PHE A 346 " pdb=" CD2 LEU A 355 " model vdw 1.756 3.860 nonbonded pdb=" O ASN A 757 " pdb=" OG1 THR A 762 " model vdw 2.173 3.040 nonbonded pdb=" O GLN B 763 " pdb=" OG1 THR B 766 " model vdw 2.215 3.040 nonbonded pdb=" O TYR A 746 " pdb=" OG1 THR A 750 " model vdw 2.226 3.040 nonbonded pdb=" O VAL B 450 " pdb=" OG1 THR B 453 " model vdw 2.228 3.040 ... (remaining 106259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 287 through 926 or resid 1020 through 1208 or resid 1301)) \ selection = (chain 'B' and (resid 287 through 345 or (resid 346 through 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 1208 or resid 1301 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.680 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.005 0.111 13318 Z= 0.319 Angle : 0.832 18.053 18065 Z= 0.456 Chirality : 0.054 0.933 2082 Planarity : 0.006 0.063 2243 Dihedral : 13.626 88.533 4775 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.22 % Allowed : 0.57 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1655 helix: 0.40 (0.16), residues: 940 sheet: -0.87 (0.47), residues: 129 loop : -2.21 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 300 HIS 0.003 0.001 HIS B 773 PHE 0.049 0.002 PHE B 728 TYR 0.024 0.002 TYR A 353 ARG 0.009 0.001 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.446 Fit side-chains REVERT: A 402 MET cc_start: 0.6509 (tmm) cc_final: 0.3596 (mmt) REVERT: A 590 PHE cc_start: 0.6053 (m-80) cc_final: 0.5678 (m-80) REVERT: B 748 TYR cc_start: 0.7324 (t80) cc_final: 0.7121 (t80) REVERT: B 1128 GLU cc_start: 0.6178 (pt0) cc_final: 0.5894 (pt0) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2126 time to fit residues: 77.0080 Evaluate side-chains 198 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 150 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13318 Z= 0.215 Angle : 0.604 12.641 18065 Z= 0.318 Chirality : 0.043 0.220 2082 Planarity : 0.005 0.060 2243 Dihedral : 6.554 83.051 1780 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.93 % Allowed : 7.53 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.53 (0.20), residues: 1655 helix: 0.73 (0.16), residues: 973 sheet: -0.90 (0.46), residues: 129 loop : -2.16 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 300 HIS 0.006 0.001 HIS A1067 PHE 0.042 0.002 PHE B 728 TYR 0.037 0.001 TYR A 739 ARG 0.010 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 1.355 Fit side-chains REVERT: A 402 MET cc_start: 0.6551 (tmm) cc_final: 0.3634 (mmt) REVERT: A 590 PHE cc_start: 0.6469 (m-80) cc_final: 0.6101 (m-80) REVERT: A 1120 GLN cc_start: 0.6573 (mm-40) cc_final: 0.6347 (mm-40) REVERT: B 368 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 748 TYR cc_start: 0.7334 (t80) cc_final: 0.7047 (t80) outliers start: 13 outliers final: 8 residues processed: 221 average time/residue: 0.2030 time to fit residues: 69.4503 Evaluate side-chains 207 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.0770 chunk 163 optimal weight: 0.9980 chunk 134 optimal weight: 0.0770 chunk 149 optimal weight: 0.0170 chunk 51 optimal weight: 0.0470 chunk 121 optimal weight: 7.9990 overall best weight: 0.1432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13318 Z= 0.155 Angle : 0.559 13.336 18065 Z= 0.292 Chirality : 0.042 0.175 2082 Planarity : 0.005 0.059 2243 Dihedral : 6.313 83.188 1780 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.36 % Allowed : 10.82 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1655 helix: 0.95 (0.16), residues: 980 sheet: -0.84 (0.45), residues: 129 loop : -2.09 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.045 0.001 PHE B 728 TYR 0.017 0.001 TYR A 353 ARG 0.007 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 223 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6453 (tmm) cc_final: 0.3733 (mmt) REVERT: A 590 PHE cc_start: 0.6622 (m-80) cc_final: 0.6235 (m-80) REVERT: A 626 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4993 (t80) REVERT: A 640 MET cc_start: 0.6134 (pmm) cc_final: 0.5541 (pmm) REVERT: B 368 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 748 TYR cc_start: 0.7287 (t80) cc_final: 0.7069 (t80) REVERT: B 776 ARG cc_start: 0.6182 (tpp80) cc_final: 0.5922 (ttm170) REVERT: B 1184 MET cc_start: 0.7373 (mmm) cc_final: 0.6930 (mmm) outliers start: 19 outliers final: 12 residues processed: 230 average time/residue: 0.2084 time to fit residues: 73.5792 Evaluate side-chains 208 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 732 TRP Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.0170 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 160 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13318 Z= 0.186 Angle : 0.556 8.633 18065 Z= 0.292 Chirality : 0.042 0.250 2082 Planarity : 0.004 0.054 2243 Dihedral : 6.202 84.538 1780 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.08 % Allowed : 12.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1655 helix: 1.08 (0.16), residues: 982 sheet: -0.91 (0.45), residues: 129 loop : -2.11 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.032 0.002 PHE B 728 TYR 0.015 0.001 TYR A 353 ARG 0.005 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6460 (tmm) cc_final: 0.3781 (mmt) REVERT: A 590 PHE cc_start: 0.6742 (m-80) cc_final: 0.6365 (m-80) REVERT: A 626 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.4943 (t80) REVERT: A 640 MET cc_start: 0.6124 (pmm) cc_final: 0.5633 (pmm) REVERT: A 678 ILE cc_start: 0.7558 (mt) cc_final: 0.7256 (mt) REVERT: B 368 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 776 ARG cc_start: 0.6414 (tpp80) cc_final: 0.6194 (ttm170) outliers start: 29 outliers final: 16 residues processed: 224 average time/residue: 0.2336 time to fit residues: 82.2807 Evaluate side-chains 213 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13318 Z= 0.300 Angle : 0.620 12.901 18065 Z= 0.322 Chirality : 0.045 0.222 2082 Planarity : 0.005 0.072 2243 Dihedral : 6.267 86.042 1780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.51 % Allowed : 13.84 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1655 helix: 0.97 (0.16), residues: 974 sheet: -1.04 (0.45), residues: 127 loop : -2.12 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 300 HIS 0.005 0.001 HIS A1067 PHE 0.030 0.002 PHE B 728 TYR 0.017 0.001 TYR A 353 ARG 0.006 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6492 (tmm) cc_final: 0.3765 (mmt) REVERT: A 590 PHE cc_start: 0.6866 (m-80) cc_final: 0.6478 (m-80) REVERT: A 626 PHE cc_start: 0.5558 (OUTLIER) cc_final: 0.5010 (t80) REVERT: A 640 MET cc_start: 0.6160 (pmm) cc_final: 0.5736 (pmm) REVERT: A 1151 ARG cc_start: 0.8273 (tpt170) cc_final: 0.8009 (tpt170) REVERT: B 297 LEU cc_start: 0.8413 (mt) cc_final: 0.8130 (pp) REVERT: B 368 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8521 (mp) outliers start: 35 outliers final: 23 residues processed: 229 average time/residue: 0.2083 time to fit residues: 73.4400 Evaluate side-chains 219 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13318 Z= 0.207 Angle : 0.597 12.887 18065 Z= 0.308 Chirality : 0.043 0.197 2082 Planarity : 0.005 0.071 2243 Dihedral : 6.176 84.690 1780 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.15 % Allowed : 15.70 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1655 helix: 1.03 (0.17), residues: 974 sheet: -0.83 (0.46), residues: 121 loop : -2.15 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 300 HIS 0.005 0.001 HIS A1067 PHE 0.037 0.002 PHE B 659 TYR 0.017 0.001 TYR A 746 ARG 0.006 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.6518 (tmm) cc_final: 0.3771 (mmt) REVERT: A 590 PHE cc_start: 0.6868 (m-80) cc_final: 0.6530 (m-80) REVERT: A 626 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4954 (t80) REVERT: A 640 MET cc_start: 0.6134 (pmm) cc_final: 0.5753 (pmm) REVERT: B 297 LEU cc_start: 0.8406 (mt) cc_final: 0.8113 (pp) REVERT: B 368 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8509 (mp) outliers start: 30 outliers final: 20 residues processed: 222 average time/residue: 0.2062 time to fit residues: 70.6244 Evaluate side-chains 213 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5902 > 50: distance: 41 - 63: 10.009 distance: 45 - 71: 10.857 distance: 48 - 49: 4.506 distance: 49 - 50: 6.096 distance: 50 - 51: 7.159 distance: 50 - 56: 9.879 distance: 51 - 79: 24.494 distance: 52 - 53: 10.668 distance: 52 - 54: 21.763 distance: 53 - 55: 11.220 distance: 56 - 57: 4.738 distance: 57 - 58: 10.468 distance: 57 - 60: 6.432 distance: 58 - 59: 27.388 distance: 58 - 63: 5.253 distance: 59 - 86: 40.686 distance: 60 - 61: 14.901 distance: 60 - 62: 25.021 distance: 63 - 64: 6.647 distance: 64 - 65: 7.247 distance: 64 - 67: 12.678 distance: 65 - 66: 4.397 distance: 65 - 71: 4.039 distance: 66 - 94: 21.292 distance: 67 - 68: 12.558 distance: 68 - 69: 16.759 distance: 68 - 70: 15.198 distance: 72 - 73: 8.291 distance: 72 - 75: 7.522 distance: 73 - 74: 25.425 distance: 73 - 79: 24.905 distance: 74 - 102: 23.978 distance: 75 - 76: 7.589 distance: 76 - 77: 14.207 distance: 76 - 78: 31.999 distance: 79 - 80: 35.615 distance: 80 - 81: 25.271 distance: 80 - 83: 11.247 distance: 81 - 82: 7.373 distance: 81 - 86: 14.778 distance: 82 - 110: 15.456 distance: 83 - 84: 21.578 distance: 83 - 85: 20.607 distance: 86 - 87: 12.255 distance: 87 - 88: 7.029 distance: 87 - 90: 8.190 distance: 88 - 89: 6.313 distance: 89 - 118: 21.312 distance: 90 - 91: 5.934 distance: 90 - 92: 16.386 distance: 91 - 93: 16.091 distance: 94 - 95: 7.503 distance: 95 - 96: 4.918 distance: 95 - 98: 6.658 distance: 96 - 97: 8.137 distance: 96 - 102: 7.897 distance: 97 - 123: 8.338 distance: 98 - 99: 11.298 distance: 99 - 100: 5.142 distance: 99 - 101: 10.081 distance: 102 - 103: 11.730 distance: 103 - 104: 5.583 distance: 103 - 106: 15.216 distance: 104 - 105: 3.089 distance: 104 - 110: 3.621 distance: 105 - 131: 12.336 distance: 107 - 108: 9.510 distance: 107 - 109: 5.491 distance: 110 - 111: 5.575 distance: 111 - 112: 8.232 distance: 111 - 114: 11.893 distance: 112 - 113: 6.801 distance: 113 - 135: 15.400 distance: 114 - 115: 5.878 distance: 115 - 116: 6.588 distance: 115 - 117: 5.751 distance: 118 - 119: 16.268 distance: 119 - 120: 9.661 distance: 119 - 122: 5.178 distance: 120 - 121: 6.715 distance: 120 - 123: 9.251 distance: 121 - 143: 4.619