Starting phenix.real_space_refine on Thu Feb 15 02:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1d_11984/02_2024/7b1d_11984.pdb" } resolution = 3.41 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= 0.012 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 47 5.16 5 C 6913 2.51 5 N 1882 2.21 5 O 2125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B ASP 706": "OD1" <-> "OD2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10967 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5573 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 33, 'TRANS': 719} Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 589 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 329 Chain: "C" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5226 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1034 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 1, 'HIS:plan': 10, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 491 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.98, per 1000 atoms: 0.55 Number of scatterers: 10967 At special positions: 0 Unit cell: (94.62, 125.33, 191.73, 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 47 16.00 O 2125 8.00 N 1882 7.00 C 6913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 561 " - pdb=" SG CYS C 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 767 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 783 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN B 481 " " NAG B 801 " - " ASN B 521 " " NAG B 802 " - " ASN B 194 " " NAG B 803 " - " ASN B 634 " " NAG C 801 " - " ASN C 194 " " NAG D 1 " - " ASN B 151 " " NAG E 1 " - " ASN C 481 " " NAG F 1 " - " ASN C 151 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 3.1 seconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 18 sheets defined 10.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.105A pdb=" N GLU B 144 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.608A pdb=" N LEU B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 3.687A pdb=" N VAL B 470 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.542A pdb=" N THR B 675 " --> pdb=" O PRO B 672 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 676 " --> pdb=" O ASN B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 716 through 723 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.179A pdb=" N LEU B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.928A pdb=" N PHE C 143 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 144 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 514 through 516 No H-bonds generated for 'chain 'C' and resid 514 through 516' Processing helix chain 'C' and resid 560 through 562 No H-bonds generated for 'chain 'C' and resid 560 through 562' Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 597 through 601 Processing helix chain 'C' and resid 603 through 607 Processing helix chain 'C' and resid 716 through 721 removed outlier: 3.882A pdb=" N ALA C 721 " --> pdb=" O ASP C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 4.282A pdb=" N SER C 747 " --> pdb=" O CYS C 743 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 748 " --> pdb=" O PRO C 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.100A pdb=" N VAL B 74 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B 102 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 155 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR B 129 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.724A pdb=" N ALA B 92 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N ALA B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY B 94 " --> pdb=" O ALA B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 137 removed outlier: 5.426A pdb=" N ILE B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 174 through 176 removed outlier: 6.795A pdb=" N LEU B 175 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 198 " --> pdb=" O SER B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 248 removed outlier: 3.523A pdb=" N GLU B 271 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 270 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 319 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 367 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU B 477 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 501 " --> pdb=" O ASN B 525 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 548 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASN B 581 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 550 " --> pdb=" O ASN B 581 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.597A pdb=" N ARG B 586 " --> pdb=" O LEU B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AA9, first strand: chain 'B' and resid 659 through 662 removed outlier: 6.852A pdb=" N LEU B 659 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 683 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 661 " --> pdb=" O LEU B 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 738 through 739 removed outlier: 3.771A pdb=" N TRP B 739 " --> pdb=" O ARG B 766 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.488A pdb=" N VAL C 74 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL C 102 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 removed outlier: 5.911A pdb=" N ILE C 136 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER C 160 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.645A pdb=" N THR C 273 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 294 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 319 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 343 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 367 " --> pdb=" O TYR C 392 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 415 " --> pdb=" O TYR C 440 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 477 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 510 through 512 removed outlier: 6.855A pdb=" N LEU C 511 " --> pdb=" O LEU C 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 523 through 525 removed outlier: 6.780A pdb=" N ILE C 548 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASN C 581 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 550 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 630 through 631 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 684 removed outlier: 6.096A pdb=" N LEU C 683 " --> pdb=" O ASP C 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 128 hydrogen bonds defined for protein. 279 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: 3.45 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3281 1.33 - 1.46: 1698 1.46 - 1.58: 6110 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 11147 Sorted by residual: bond pdb=" N CYS C 561 " pdb=" CA CYS C 561 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.21e-02 6.83e+03 1.50e+01 bond pdb=" N ILE C 705 " pdb=" CA ILE C 705 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE C 704 " pdb=" CA ILE C 704 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.17e-02 7.31e+03 9.77e+00 bond pdb=" N ILE C 531 " pdb=" CA ILE C 531 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.11e+00 bond pdb=" C PRO C 590 " pdb=" O PRO C 590 " ideal model delta sigma weight residual 1.243 1.218 0.025 8.50e-03 1.38e+04 8.92e+00 ... (remaining 11142 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 243 105.96 - 112.96: 6180 112.96 - 119.97: 3601 119.97 - 126.98: 5131 126.98 - 133.98: 88 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N CYS C 561 " pdb=" CA CYS C 561 " pdb=" C CYS C 561 " ideal model delta sigma weight residual 111.28 116.68 -5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N PRO C 591 " pdb=" CA PRO C 591 " pdb=" C PRO C 591 " ideal model delta sigma weight residual 113.53 107.03 6.50 1.39e+00 5.18e-01 2.19e+01 angle pdb=" N LYS C 565 " pdb=" CA LYS C 565 " pdb=" C LYS C 565 " ideal model delta sigma weight residual 111.69 106.21 5.48 1.23e+00 6.61e-01 1.98e+01 angle pdb=" CA LEU C 557 " pdb=" C LEU C 557 " pdb=" O LEU C 557 " ideal model delta sigma weight residual 122.27 117.51 4.76 1.16e+00 7.43e-01 1.69e+01 angle pdb=" O LEU C 446 " pdb=" C LEU C 446 " pdb=" N ALA C 447 " ideal model delta sigma weight residual 122.87 118.03 4.84 1.23e+00 6.61e-01 1.55e+01 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6456 17.67 - 35.34: 422 35.34 - 53.01: 85 53.01 - 70.68: 18 70.68 - 88.35: 10 Dihedral angle restraints: 6991 sinusoidal: 2542 harmonic: 4449 Sorted by residual: dihedral pdb=" CB CYS C 741 " pdb=" SG CYS C 741 " pdb=" SG CYS C 767 " pdb=" CB CYS C 767 " ideal model delta sinusoidal sigma weight residual -86.00 -174.35 88.35 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS C 78 " pdb=" SG CYS C 78 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual -86.00 -171.99 85.99 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C 559 " pdb=" SG CYS C 559 " pdb=" SG CYS C 587 " pdb=" CB CYS C 587 " ideal model delta sinusoidal sigma weight residual 93.00 165.32 -72.32 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 6988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1456 0.050 - 0.099: 331 0.099 - 0.149: 87 0.149 - 0.198: 11 0.198 - 0.248: 2 Chirality restraints: 1887 Sorted by residual: chirality pdb=" CB ILE B 548 " pdb=" CA ILE B 548 " pdb=" CG1 ILE B 548 " pdb=" CG2 ILE B 548 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA CYS B 57 " pdb=" N CYS B 57 " pdb=" C CYS B 57 " pdb=" CB CYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 151 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1884 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 446 " -0.039 2.00e-02 2.50e+03 7.56e-02 5.71e+01 pdb=" C LEU C 446 " 0.131 2.00e-02 2.50e+03 pdb=" O LEU C 446 " -0.049 2.00e-02 2.50e+03 pdb=" N ALA C 447 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 671 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO B 672 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 561 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C CYS C 561 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS C 561 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 562 " 0.012 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 11344 3.28 - 3.82: 17340 3.82 - 4.36: 20683 4.36 - 4.90: 35275 Nonbonded interactions: 85351 Sorted by model distance: nonbonded pdb=" O ASN B 506 " pdb=" ND2 ASN B 529 " model vdw 2.197 2.520 nonbonded pdb=" OD1 ASN B 506 " pdb=" ND2 ASN B 529 " model vdw 2.199 2.520 nonbonded pdb=" O ARG C 249 " pdb=" OG1 THR C 273 " model vdw 2.202 2.440 nonbonded pdb=" OE2 GLU C 207 " pdb=" NE2 GLN C 209 " model vdw 2.256 2.520 nonbonded pdb=" O ASP C 108 " pdb=" OH TYR C 142 " model vdw 2.257 2.440 ... (remaining 85346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 33 or (resid 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 83 or (resid 84 and (name N or name CA or nam \ e C or name O or name CB )) or resid 85 or (resid 86 and (name N or name CA or n \ ame C or name O or name CB )) or resid 87 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 132 or (resid \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throug \ h 162 or (resid 163 through 164 and (name N or name CA or name C or name O or na \ me CB )) or resid 165 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 through 189 or (resid 190 through 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 8 through 229 or (resid 230 and (name N or name CA or name C or name O or name C \ B )) or resid 231 through 256 or (resid 257 through 259 and (name N or name CA o \ r name C or name O or name CB )) or resid 260 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB )) or resid 272 through 406 or (re \ sid 407 and (name N or name CA or name C or name O or name CB )) or resid 408 th \ rough 447 or (resid 448 through 452 and (name N or name CA or name C or name O o \ r name CB )) or resid 453 through 468 or (resid 469 through 473 and (name N or n \ ame CA or name C or name O or name CB )) or resid 474 through 487 or (resid 488 \ through 490 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 1 or (resid 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ me CB )) or resid 518 through 539 or (resid 540 through 543 and (name N or name \ CA or name C or name O or name CB )) or resid 544 through 557 or (resid 558 and \ (name N or name CA or name C or name O or name CB )) or resid 559 or (resid 560 \ and (name N or name CA or name C or name O or name CB )) or resid 561 through 56 \ 3 or (resid 564 through 576 and (name N or name CA or name C or name O or name C \ B )) or resid 577 through 580 or (resid 581 and (name N or name CA or name C or \ name O or name CB )) or resid 582 or (resid 583 through 584 and (name N or name \ CA or name C or name O or name CB )) or resid 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 or (resid 588 through 589 \ and (name N or name CA or name C or name O or name CB )) or resid 590 through 59 \ 1 or (resid 592 through 593 and (name N or name CA or name C or name O or name C \ B )) or resid 594 or (resid 595 through 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 600 or (resid 601 through 607 and (nam \ e N or name CA or name C or name O or name CB )) or resid 608 or (resid 609 thro \ ugh 615 and (name N or name CA or name C or name O or name CB )) or resid 616 th \ rough 623 or (resid 624 through 634 and (name N or name CA or name C or name O o \ r name CB )) or resid 635 or (resid 636 and (name N or name CA or name C or name \ O or name CB )) or resid 637 or (resid 638 and (name N or name CA or name C or \ name O or name CB )) or resid 639 through 645 or (resid 646 and (name N or name \ CA or name C or name O or name CB )) or resid 647 or (resid 648 and (name N or n \ ame CA or name C or name O or name CB )) or resid 649 or (resid 650 through 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 66 \ 8 or (resid 669 through 671 and (name N or name CA or name C or name O or name C \ B )) or resid 672 or (resid 673 through 694 and (name N or name CA or name C or \ name O or name CB )) or resid 695 through 696 or (resid 697 through 698 and (nam \ e N or name CA or name C or name O or name CB )) or resid 699 or (resid 700 thro \ ugh 740 and (name N or name CA or name C or name O or name CB )) or resid 741 th \ rough 777 or (resid 778 through 782 and (name N or name CA or name C or name O o \ r name CB )) or resid 783 through 784 or resid 801)) selection = (chain 'C' and (resid 33 through 36 or (resid 37 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 50 or (resid 51 through \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 59 or (resid 60 through 61 and (name N or name CA or name C or name O or name C \ B )) or resid 62 through 66 or (resid 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 79 or (resid 80 through 81 and (name N or \ name CA or name C or name O or name CB )) or resid 82 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 24 \ 8 or (resid 249 and (name N or name CA or name C or name O or name CB )) or resi \ d 250 through 251 or (resid 252 and (name N or name CA or name C or name O or na \ me CB )) or resid 253 through 272 or (resid 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 354 or (resid 355 through 356 and \ (name N or name CA or name C or name O or name CB )) or resid 357 through 385 or \ (resid 386 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 7 through 454 or (resid 455 through 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 through 489 or (resid 490 and (name N or name CA o \ r name C or name O or name CB )) or resid 491 through 784 or resid 801)) } 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=0.00 max=1.00 mean=0.99 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: 3.880 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: 12.060 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.580 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11147 Z= 0.288 Angle : 0.707 7.794 15243 Z= 0.418 Chirality : 0.047 0.248 1887 Planarity : 0.004 0.076 2005 Dihedral : 12.557 85.658 4023 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.29 % Allowed : 0.48 % Favored : 99.23 % 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: -1.47 (0.21), residues: 1501 helix: -0.12 (0.64), residues: 71 sheet: -1.43 (0.36), residues: 230 loop : -0.99 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 491 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE C 85 TYR 0.014 0.001 TYR B 138 ARG 0.002 0.000 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 1.197 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.1428 time to fit residues: 8.9965 Evaluate side-chains 25 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.4980 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 11147 Z= 0.520 Angle : 0.753 8.341 15243 Z= 0.368 Chirality : 0.047 0.203 1887 Planarity : 0.004 0.069 2005 Dihedral : 6.352 49.077 1825 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.57 % Allowed : 5.46 % Favored : 93.97 % 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: -1.59 (0.21), residues: 1501 helix: -0.91 (0.52), residues: 85 sheet: -1.56 (0.34), residues: 247 loop : -1.00 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 491 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.002 PHE B 656 TYR 0.020 0.002 TYR C 440 ARG 0.005 0.001 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 1.255 Fit side-chains REVERT: C 441 MET cc_start: 0.9072 (mmm) cc_final: 0.8694 (mmm) REVERT: C 594 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7108 (tp) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.1287 time to fit residues: 7.6302 Evaluate side-chains 29 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.0020 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 30.0000 chunk 147 optimal weight: 50.0000 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11147 Z= 0.143 Angle : 0.536 7.789 15243 Z= 0.272 Chirality : 0.042 0.158 1887 Planarity : 0.003 0.061 2005 Dihedral : 5.620 49.209 1825 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.77 % Allowed : 7.18 % Favored : 92.05 % 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: -1.28 (0.21), residues: 1501 helix: 0.10 (0.60), residues: 79 sheet: -1.36 (0.34), residues: 249 loop : -0.84 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 491 HIS 0.003 0.001 HIS B 395 PHE 0.014 0.001 PHE C 85 TYR 0.009 0.001 TYR B 56 ARG 0.001 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 1.251 Fit side-chains REVERT: B 669 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7515 (m) REVERT: C 441 MET cc_start: 0.9114 (mmm) cc_final: 0.8745 (mmm) REVERT: C 594 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6949 (tp) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.1586 time to fit residues: 10.3492 Evaluate side-chains 31 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 40.0000 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN C 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 11147 Z= 0.406 Angle : 0.653 8.630 15243 Z= 0.320 Chirality : 0.045 0.171 1887 Planarity : 0.004 0.067 2005 Dihedral : 5.826 49.261 1825 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.92 % Allowed : 8.14 % Favored : 89.94 % 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: -1.36 (0.22), residues: 1501 helix: -0.01 (0.58), residues: 79 sheet: -1.50 (0.34), residues: 250 loop : -0.86 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 491 HIS 0.006 0.001 HIS B 54 PHE 0.014 0.001 PHE B 656 TYR 0.014 0.002 TYR C 440 ARG 0.005 0.000 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 24 time to evaluate : 1.126 Fit side-chains REVERT: B 669 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (t) REVERT: C 360 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8385 (t0) REVERT: C 441 MET cc_start: 0.9097 (mmm) cc_final: 0.8734 (mmm) REVERT: C 594 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7286 (tp) outliers start: 20 outliers final: 13 residues processed: 40 average time/residue: 0.1432 time to fit residues: 11.0715 Evaluate side-chains 40 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 24 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 HIS ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 11147 Z= 0.580 Angle : 0.775 9.499 15243 Z= 0.378 Chirality : 0.047 0.186 1887 Planarity : 0.004 0.062 2005 Dihedral : 6.492 50.582 1825 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.07 % Allowed : 9.29 % Favored : 87.64 % 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: -1.59 (0.22), residues: 1501 helix: -0.45 (0.55), residues: 79 sheet: -1.48 (0.36), residues: 246 loop : -1.06 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 491 HIS 0.005 0.002 HIS B 54 PHE 0.024 0.002 PHE C 60 TYR 0.019 0.002 TYR C 440 ARG 0.006 0.001 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 23 time to evaluate : 0.942 Fit side-chains REVERT: B 180 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 411 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8764 (t0) REVERT: C 67 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7171 (p0) REVERT: C 360 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8324 (t0) REVERT: C 594 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7454 (tp) outliers start: 32 outliers final: 22 residues processed: 52 average time/residue: 0.1216 time to fit residues: 11.5343 Evaluate side-chains 50 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 23 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 145 optimal weight: 0.0570 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: