Starting phenix.real_space_refine on Tue May 13 00:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.map" model { file = "/net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dz2_47323/05_2025/9dz2_47323.cif" } resolution = 3.31 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= 0.011 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 44 5.16 5 C 6092 2.51 5 N 1615 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9523 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1723 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "I" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1198 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 12, 'TRANS': 144} Chain: "J" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 835 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1230 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 13, 'TRANS': 147} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 812 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1701 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 2 Chain: "E" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1189 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 12, 'TRANS': 143} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 835 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 6.41, per 1000 atoms: 0.67 Number of scatterers: 9523 At special positions: 0 Unit cell: (118.635, 101.813, 141.653, 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 44 16.00 O 1772 8.00 N 1615 7.00 C 6092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 516 " - pdb=" SG CYS C 533 " distance=2.02 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS J 609 " distance=2.04 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 135 " distance=2.03 Simple disulfide: pdb=" SG CYS I 121 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 511 " - pdb=" SG CYS J 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 601 " - pdb=" SG CYS J 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS D 468 " - pdb=" SG CYS D 479 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 533 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 23 sheets defined 25.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.777A pdb=" N HIS C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 removed outlier: 3.954A pdb=" N ILE C 467 " --> pdb=" O THR C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 489 Processing helix chain 'C' and resid 508 through 517 removed outlier: 3.680A pdb=" N CYS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.503A pdb=" N VAL C 546 " --> pdb=" O PHE C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 554 through 558 Processing helix chain 'C' and resid 573 through 593 Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 71 through 74 Processing helix chain 'I' and resid 78 through 83 removed outlier: 3.516A pdb=" N THR I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 559 removed outlier: 3.552A pdb=" N VAL J 555 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY J 557 " --> pdb=" O ALA J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 576 removed outlier: 4.563A pdb=" N ALA J 568 " --> pdb=" O GLU J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 599 removed outlier: 4.371A pdb=" N GLY J 599 " --> pdb=" O ARG J 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 removed outlier: 4.089A pdb=" N GLY A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'B' and resid 554 through 576 removed outlier: 3.619A pdb=" N LEU B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'D' and resid 391 through 398 removed outlier: 3.552A pdb=" N PHE D 395 " --> pdb=" O GLU D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 Processing helix chain 'D' and resid 436 through 452 removed outlier: 3.829A pdb=" N HIS D 441 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 removed outlier: 3.929A pdb=" N ILE D 467 " --> pdb=" O THR D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 489 Processing helix chain 'D' and resid 508 through 517 Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.653A pdb=" N VAL D 546 " --> pdb=" O PHE D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'D' and resid 573 through 593 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 removed outlier: 4.052A pdb=" N GLY E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.512A pdb=" N GLN F 560 " --> pdb=" O CYS F 556 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 561 " --> pdb=" O GLY F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 576 removed outlier: 4.504A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing sheet with id=AA1, first strand: chain 'C' and resid 563 through 568 removed outlier: 4.462A pdb=" N ILE C 563 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 408 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 602 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 411 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 600 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 418 through 420 Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'C' and resid 547 through 548 Processing sheet with id=AA5, first strand: chain 'I' and resid 43 through 46 Processing sheet with id=AA6, first strand: chain 'I' and resid 43 through 46 removed outlier: 3.548A pdb=" N LEU I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL I 96 " --> pdb=" O THR J 581 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AA8, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AA9, first strand: chain 'I' and resid 110 through 114 removed outlier: 6.313A pdb=" N ASN I 110 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY I 143 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU I 112 " --> pdb=" O GLY I 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.443A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.443A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB4, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB5, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.998A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 563 through 567 removed outlier: 4.501A pdb=" N ILE D 563 " --> pdb=" O LEU D 408 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 408 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 411 " --> pdb=" O THR D 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 600 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AB8, first strand: chain 'D' and resid 455 through 457 Processing sheet with id=AB9, first strand: chain 'D' and resid 547 through 548 Processing sheet with id=AC1, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.253A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.253A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER E 98 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC4, first strand: chain 'E' and resid 101 through 103 Processing sheet with id=AC5, first strand: chain 'E' and resid 105 through 114 removed outlier: 7.061A pdb=" N GLU E 106 " --> pdb=" O CYS E 135 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 762 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: 2.61 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3116 1.35 - 1.47: 2397 1.47 - 1.59: 4215 1.59 - 1.71: 1 1.71 - 1.84: 50 Bond restraints: 9779 Sorted by residual: bond pdb=" CG PRO I 124 " pdb=" CD PRO I 124 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.51e+01 bond pdb=" C PRO C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.334 1.361 -0.027 8.40e-03 1.42e+04 1.03e+01 bond pdb=" N ILE J 603 " pdb=" CA ILE J 603 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.54e+00 bond pdb=" CB PRO I 124 " pdb=" CG PRO I 124 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.40e+00 bond pdb=" CA ILE F 610 " pdb=" CB ILE F 610 " ideal model delta sigma weight residual 1.540 1.564 -0.024 1.36e-02 5.41e+03 3.16e+00 ... (remaining 9774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 13086 2.44 - 4.88: 201 4.88 - 7.33: 33 7.33 - 9.77: 4 9.77 - 12.21: 2 Bond angle restraints: 13326 Sorted by residual: angle pdb=" CA PRO I 124 " pdb=" N PRO I 124 " pdb=" CD PRO I 124 " ideal model delta sigma weight residual 112.00 99.79 12.21 1.40e+00 5.10e-01 7.61e+01 angle pdb=" N PRO I 124 " pdb=" CD PRO I 124 " pdb=" CG PRO I 124 " ideal model delta sigma weight residual 103.20 93.22 9.98 1.50e+00 4.44e-01 4.43e+01 angle pdb=" CA ILE F 610 " pdb=" CB ILE F 610 " pdb=" CG2 ILE F 610 " ideal model delta sigma weight residual 110.50 116.91 -6.41 1.70e+00 3.46e-01 1.42e+01 angle pdb=" CA ARG J 595 " pdb=" CB ARG J 595 " pdb=" CG ARG J 595 " ideal model delta sigma weight residual 114.10 107.09 7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLN E 142 " pdb=" CB GLN E 142 " pdb=" CG GLN E 142 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.14e+01 ... (remaining 13321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5212 17.95 - 35.90: 475 35.90 - 53.85: 76 53.85 - 71.80: 27 71.80 - 89.76: 12 Dihedral angle restraints: 5802 sinusoidal: 2321 harmonic: 3481 Sorted by residual: dihedral pdb=" CB CYS F 601 " pdb=" SG CYS F 601 " pdb=" SG CYS F 608 " pdb=" CB CYS F 608 " ideal model delta sinusoidal sigma weight residual 93.00 37.59 55.41 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS I 53 " pdb=" SG CYS I 53 " pdb=" SG CYS J 609 " pdb=" CB CYS J 609 " ideal model delta sinusoidal sigma weight residual 93.00 147.54 -54.54 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CB CYS C 516 " pdb=" SG CYS C 516 " pdb=" SG CYS C 533 " pdb=" CB CYS C 533 " ideal model delta sinusoidal sigma weight residual -86.00 -46.89 -39.11 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 5799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1117 0.047 - 0.095: 248 0.095 - 0.142: 85 0.142 - 0.190: 3 0.190 - 0.237: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CB ILE F 610 " pdb=" CA ILE F 610 " pdb=" CG1 ILE F 610 " pdb=" CG2 ILE F 610 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE E 79 " pdb=" CA ILE E 79 " pdb=" CG1 ILE E 79 " pdb=" CG2 ILE E 79 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA CYS C 516 " pdb=" N CYS C 516 " pdb=" C CYS C 516 " pdb=" CB CYS C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1452 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 123 " 0.074 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO I 124 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 611 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 612 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 612 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 612 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 142 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLN E 142 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN E 142 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY E 143 " 0.012 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 376 2.72 - 3.26: 9219 3.26 - 3.81: 14545 3.81 - 4.35: 18635 4.35 - 4.90: 31351 Nonbonded interactions: 74126 Sorted by model distance: nonbonded pdb=" NZ LYS E 64 " pdb=" OE1 GLU E 100 " model vdw 2.174 3.120 nonbonded pdb=" O GLY J 598 " pdb=" NH1 ARG F 596 " model vdw 2.224 3.120 nonbonded pdb=" O PRO D 430 " pdb=" ND2 ASN D 556 " model vdw 2.248 3.120 nonbonded pdb=" O LEU D 472 " pdb=" N ASN D 476 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP E 78 " pdb=" N ILE E 79 " model vdw 2.291 3.120 ... (remaining 74121 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 32 through 187) selection = chain 'E' selection = (chain 'I' and resid 32 through 187) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 510 through 523 or resid 527 through 614)) selection = (chain 'J' and (resid 510 through 523 or resid 527 through 614)) } ncs_group { reference = (chain 'C' and (resid 390 through 399 or resid 403 through 604)) selection = chain 'D' } 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: 2.130 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 0.132 9798 Z= 0.160 Angle : 0.744 12.211 13364 Z= 0.395 Chirality : 0.046 0.237 1455 Planarity : 0.005 0.104 1742 Dihedral : 14.552 89.756 3515 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.26 % Favored : 93.15 % Rotamer: Outliers : 0.49 % Allowed : 7.29 % Favored : 92.23 % 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: -2.10 (0.23), residues: 1183 helix: -0.86 (0.33), residues: 226 sheet: -0.94 (0.32), residues: 248 loop : -1.80 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 86 HIS 0.006 0.001 HIS C 512 PHE 0.022 0.002 PHE C 513 TYR 0.027 0.002 TYR C 509 ARG 0.007 0.001 ARG F 602 Details of bonding type rmsd hydrogen bonds : bond 0.25896 ( 284) hydrogen bonds : angle 9.00938 ( 762) SS BOND : bond 0.00428 ( 19) SS BOND : angle 1.79501 ( 38) covalent geometry : bond 0.00360 ( 9779) covalent geometry : angle 0.73915 (13326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 237 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 GLN cc_start: 0.7643 (tt0) cc_final: 0.7155 (tt0) REVERT: D 514 LEU cc_start: 0.5846 (mt) cc_final: 0.5591 (tt) REVERT: E 142 GLN cc_start: 0.7633 (pm20) cc_final: 0.7192 (pm20) REVERT: F 612 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7925 (Cg_exo) outliers start: 5 outliers final: 1 residues processed: 240 average time/residue: 0.2367 time to fit residues: 76.2296 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 503 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** I 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 GLN ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 ASN E 50 GLN E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.166012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110976 restraints weight = 21614.677| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.69 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9798 Z= 0.184 Angle : 0.716 8.074 13364 Z= 0.376 Chirality : 0.046 0.220 1455 Planarity : 0.005 0.049 1742 Dihedral : 5.403 59.045 1303 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.44 % Favored : 91.80 % Rotamer: Outliers : 2.24 % Allowed : 12.63 % Favored : 85.13 % 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: -1.87 (0.23), residues: 1183 helix: -0.19 (0.34), residues: 223 sheet: -1.07 (0.29), residues: 277 loop : -1.71 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.008 0.001 HIS D 510 PHE 0.018 0.002 PHE C 395 TYR 0.019 0.001 TYR C 555 ARG 0.006 0.001 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 284) hydrogen bonds : angle 6.02240 ( 762) SS BOND : bond 0.00477 ( 19) SS BOND : angle 1.06761 ( 38) covalent geometry : bond 0.00423 ( 9779) covalent geometry : angle 0.71498 (13326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7868 (pt) cc_final: 0.7335 (tp) REVERT: C 555 TYR cc_start: 0.8307 (m-80) cc_final: 0.8004 (m-10) REVERT: I 142 GLN cc_start: 0.7639 (pp30) cc_final: 0.7283 (pp30) REVERT: J 551 GLN cc_start: 0.8015 (tt0) cc_final: 0.7733 (mt0) REVERT: A 64 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8210 (mmmm) REVERT: E 120 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7629 (mt-10) REVERT: E 142 GLN cc_start: 0.7381 (pm20) cc_final: 0.7144 (pm20) REVERT: F 596 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7697 (mtp180) outliers start: 23 outliers final: 15 residues processed: 172 average time/residue: 0.2020 time to fit residues: 49.0934 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 590 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 50.0000 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN C 492 HIS J 514 ASN J 549 HIS ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS F 563 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.165880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111312 restraints weight = 21867.924| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.69 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9798 Z= 0.171 Angle : 0.637 7.143 13364 Z= 0.336 Chirality : 0.045 0.242 1455 Planarity : 0.004 0.045 1742 Dihedral : 5.126 57.434 1303 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.69 % Favored : 91.63 % Rotamer: Outliers : 2.53 % Allowed : 13.90 % Favored : 83.58 % 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: -1.82 (0.24), residues: 1183 helix: 0.00 (0.35), residues: 226 sheet: -1.08 (0.30), residues: 278 loop : -1.72 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 86 HIS 0.017 0.001 HIS F 524 PHE 0.019 0.002 PHE F 592 TYR 0.012 0.001 TYR F 582 ARG 0.005 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 284) hydrogen bonds : angle 5.64510 ( 762) SS BOND : bond 0.00355 ( 19) SS BOND : angle 1.03866 ( 38) covalent geometry : bond 0.00394 ( 9779) covalent geometry : angle 0.63514 (13326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7848 (pt) cc_final: 0.7347 (tp) REVERT: I 100 GLU cc_start: 0.8269 (mp0) cc_final: 0.7704 (mp0) REVERT: I 140 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8907 (mmtm) REVERT: I 142 GLN cc_start: 0.7837 (pp30) cc_final: 0.7397 (pp30) REVERT: J 551 GLN cc_start: 0.8036 (tt0) cc_final: 0.7713 (mt0) REVERT: A 64 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8225 (mmmm) REVERT: B 549 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (t-90) REVERT: D 514 LEU cc_start: 0.7185 (mt) cc_final: 0.6901 (mt) REVERT: E 120 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E 142 GLN cc_start: 0.7544 (pm20) cc_final: 0.7305 (pm20) REVERT: F 544 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8249 (p) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.2043 time to fit residues: 48.2877 Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 549 HIS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN B 549 HIS ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.164460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109827 restraints weight = 21573.787| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.66 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9798 Z= 0.159 Angle : 0.616 7.180 13364 Z= 0.324 Chirality : 0.044 0.239 1455 Planarity : 0.004 0.041 1742 Dihedral : 4.951 53.744 1303 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.02 % Favored : 92.31 % Rotamer: Outliers : 2.43 % Allowed : 14.67 % Favored : 82.90 % 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: -1.77 (0.23), residues: 1183 helix: 0.22 (0.35), residues: 226 sheet: -1.03 (0.31), residues: 260 loop : -1.76 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 86 HIS 0.012 0.001 HIS C 492 PHE 0.012 0.001 PHE C 542 TYR 0.011 0.001 TYR F 582 ARG 0.003 0.000 ARG J 602 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 284) hydrogen bonds : angle 5.44006 ( 762) SS BOND : bond 0.00246 ( 19) SS BOND : angle 0.94367 ( 38) covalent geometry : bond 0.00366 ( 9779) covalent geometry : angle 0.61435 (13326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7908 (pt) cc_final: 0.7407 (tp) REVERT: C 481 ILE cc_start: 0.1901 (mm) cc_final: 0.1324 (mm) REVERT: C 555 TYR cc_start: 0.8194 (m-10) cc_final: 0.7891 (m-10) REVERT: I 100 GLU cc_start: 0.8323 (mp0) cc_final: 0.7744 (mp0) REVERT: I 140 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8923 (mmtm) REVERT: I 142 GLN cc_start: 0.7934 (pp30) cc_final: 0.7175 (pp30) REVERT: J 529 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8652 (tp) REVERT: J 551 GLN cc_start: 0.8010 (tt0) cc_final: 0.7754 (mt0) REVERT: A 64 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8259 (mmmm) REVERT: A 115 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8673 (ptpp) REVERT: D 514 LEU cc_start: 0.7273 (mt) cc_final: 0.7002 (mt) REVERT: E 56 HIS cc_start: 0.8308 (m-70) cc_final: 0.8044 (m90) REVERT: E 142 GLN cc_start: 0.7629 (pm20) cc_final: 0.7368 (pm20) REVERT: F 544 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8252 (p) outliers start: 25 outliers final: 20 residues processed: 170 average time/residue: 0.2197 time to fit residues: 53.3967 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 529 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 544 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS I 62 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 523 GLN F 524 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.164216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109427 restraints weight = 21629.883| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.66 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9798 Z= 0.157 Angle : 0.610 8.140 13364 Z= 0.320 Chirality : 0.044 0.236 1455 Planarity : 0.004 0.039 1742 Dihedral : 4.861 50.430 1303 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.27 % Favored : 92.05 % Rotamer: Outliers : 3.30 % Allowed : 15.06 % Favored : 81.63 % 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: -1.78 (0.23), residues: 1183 helix: -0.09 (0.33), residues: 246 sheet: -0.80 (0.32), residues: 243 loop : -1.79 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.017 0.001 HIS F 524 PHE 0.010 0.001 PHE C 504 TYR 0.010 0.001 TYR F 582 ARG 0.003 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 284) hydrogen bonds : angle 5.28290 ( 762) SS BOND : bond 0.00241 ( 19) SS BOND : angle 1.10622 ( 38) covalent geometry : bond 0.00363 ( 9779) covalent geometry : angle 0.60779 (13326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7957 (pt) cc_final: 0.7450 (tp) REVERT: C 481 ILE cc_start: 0.1863 (mm) cc_final: 0.1412 (mm) REVERT: I 100 GLU cc_start: 0.8335 (mp0) cc_final: 0.7797 (mp0) REVERT: I 140 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8931 (mmtm) REVERT: I 142 GLN cc_start: 0.7993 (pp30) cc_final: 0.7247 (pp30) REVERT: J 551 GLN cc_start: 0.8121 (tt0) cc_final: 0.7820 (mt0) REVERT: A 64 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8289 (mmmm) REVERT: A 115 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8649 (ptpp) REVERT: B 603 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8207 (tp) REVERT: D 514 LEU cc_start: 0.7303 (mt) cc_final: 0.7040 (mt) REVERT: E 142 GLN cc_start: 0.7656 (pm20) cc_final: 0.7300 (pm20) REVERT: E 172 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8217 (ttp80) outliers start: 34 outliers final: 24 residues processed: 181 average time/residue: 0.2182 time to fit residues: 55.1856 Evaluate side-chains 178 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 0.0170 chunk 23 optimal weight: 0.0570 chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN B 613 HIS E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.163061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107059 restraints weight = 21663.183| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.68 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9798 Z= 0.174 Angle : 0.611 7.471 13364 Z= 0.320 Chirality : 0.045 0.241 1455 Planarity : 0.004 0.038 1742 Dihedral : 4.748 47.191 1303 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.44 % Favored : 91.89 % Rotamer: Outliers : 3.21 % Allowed : 16.62 % Favored : 80.17 % 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: -1.78 (0.23), residues: 1183 helix: -0.11 (0.33), residues: 248 sheet: -0.82 (0.32), residues: 244 loop : -1.77 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.004 0.001 HIS D 510 PHE 0.011 0.001 PHE C 504 TYR 0.010 0.001 TYR C 487 ARG 0.003 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 284) hydrogen bonds : angle 5.26558 ( 762) SS BOND : bond 0.00233 ( 19) SS BOND : angle 0.87914 ( 38) covalent geometry : bond 0.00405 ( 9779) covalent geometry : angle 0.61041 (13326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1796 (mm) cc_final: 0.1405 (mm) REVERT: C 499 LYS cc_start: 0.8765 (tptt) cc_final: 0.8552 (tptt) REVERT: C 569 ASN cc_start: 0.4541 (m-40) cc_final: 0.4279 (m-40) REVERT: I 100 GLU cc_start: 0.8362 (mp0) cc_final: 0.7851 (mp0) REVERT: I 140 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8950 (mmtm) REVERT: I 142 GLN cc_start: 0.8046 (pp30) cc_final: 0.7280 (pp30) REVERT: J 551 GLN cc_start: 0.8121 (tt0) cc_final: 0.7826 (mt0) REVERT: J 600 THR cc_start: 0.7659 (p) cc_final: 0.7260 (p) REVERT: J 610 ILE cc_start: 0.8538 (mt) cc_final: 0.8206 (mm) REVERT: A 64 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8320 (mmmm) REVERT: A 106 GLU cc_start: 0.8308 (tp30) cc_final: 0.8100 (tp30) REVERT: B 603 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8146 (tp) REVERT: D 514 LEU cc_start: 0.7274 (mt) cc_final: 0.6992 (mt) REVERT: E 56 HIS cc_start: 0.8401 (m90) cc_final: 0.8012 (m90) REVERT: E 142 GLN cc_start: 0.7629 (pm20) cc_final: 0.7199 (pm20) outliers start: 33 outliers final: 27 residues processed: 171 average time/residue: 0.2227 time to fit residues: 52.8804 Evaluate side-chains 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 511 CYS Chi-restraints excluded: chain J residue 544 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 544 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN I 175 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.163995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108599 restraints weight = 21696.693| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.71 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9798 Z= 0.136 Angle : 0.590 7.178 13364 Z= 0.310 Chirality : 0.044 0.235 1455 Planarity : 0.004 0.038 1742 Dihedral : 4.434 20.195 1301 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.52 % Favored : 91.80 % Rotamer: Outliers : 3.30 % Allowed : 16.62 % Favored : 80.08 % 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: -1.68 (0.23), residues: 1183 helix: 0.02 (0.33), residues: 248 sheet: -0.81 (0.32), residues: 244 loop : -1.71 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.011 0.001 HIS F 524 PHE 0.032 0.001 PHE F 592 TYR 0.009 0.001 TYR C 487 ARG 0.007 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 284) hydrogen bonds : angle 5.13812 ( 762) SS BOND : bond 0.00187 ( 19) SS BOND : angle 0.71003 ( 38) covalent geometry : bond 0.00314 ( 9779) covalent geometry : angle 0.59010 (13326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1830 (mm) cc_final: 0.1440 (mm) REVERT: C 569 ASN cc_start: 0.4551 (m-40) cc_final: 0.4269 (m-40) REVERT: I 86 TRP cc_start: 0.7960 (p90) cc_final: 0.7648 (p90) REVERT: I 100 GLU cc_start: 0.8390 (mp0) cc_final: 0.7865 (mp0) REVERT: I 140 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8935 (mmtm) REVERT: I 142 GLN cc_start: 0.8072 (pp30) cc_final: 0.7296 (pp30) REVERT: J 551 GLN cc_start: 0.8098 (tt0) cc_final: 0.7845 (mt0) REVERT: J 610 ILE cc_start: 0.8564 (mt) cc_final: 0.8248 (mm) REVERT: A 64 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8344 (mmmm) REVERT: A 106 GLU cc_start: 0.8247 (tp30) cc_final: 0.7994 (tp30) REVERT: D 514 LEU cc_start: 0.7309 (mt) cc_final: 0.6917 (mt) REVERT: D 556 ASN cc_start: 0.4852 (OUTLIER) cc_final: 0.4335 (p0) REVERT: E 140 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8707 (mmmt) REVERT: E 142 GLN cc_start: 0.7609 (pm20) cc_final: 0.7229 (pm20) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.2097 time to fit residues: 51.6608 Evaluate side-chains 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 511 CYS Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 0.0270 chunk 84 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS I 50 GLN E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110229 restraints weight = 21759.267| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.70 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9798 Z= 0.117 Angle : 0.582 7.387 13364 Z= 0.304 Chirality : 0.043 0.226 1455 Planarity : 0.004 0.040 1742 Dihedral : 4.290 19.513 1301 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.76 % Favored : 92.56 % Rotamer: Outliers : 2.62 % Allowed : 17.69 % Favored : 79.69 % 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: -1.61 (0.23), residues: 1183 helix: 0.12 (0.33), residues: 247 sheet: -0.88 (0.31), residues: 259 loop : -1.64 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.003 0.000 HIS D 510 PHE 0.009 0.001 PHE B 592 TYR 0.009 0.001 TYR C 487 ARG 0.006 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 284) hydrogen bonds : angle 4.95181 ( 762) SS BOND : bond 0.00181 ( 19) SS BOND : angle 0.66277 ( 38) covalent geometry : bond 0.00265 ( 9779) covalent geometry : angle 0.58175 (13326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1907 (mm) cc_final: 0.1536 (mm) REVERT: C 569 ASN cc_start: 0.4558 (m-40) cc_final: 0.4256 (m-40) REVERT: I 86 TRP cc_start: 0.7936 (p90) cc_final: 0.7678 (p90) REVERT: I 100 GLU cc_start: 0.8434 (mp0) cc_final: 0.7929 (mp0) REVERT: I 140 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8952 (mmtm) REVERT: I 142 GLN cc_start: 0.8099 (pp30) cc_final: 0.7405 (pp30) REVERT: J 551 GLN cc_start: 0.8080 (tt0) cc_final: 0.7844 (mt0) REVERT: J 564 GLU cc_start: 0.8231 (mp0) cc_final: 0.7956 (mp0) REVERT: J 600 THR cc_start: 0.7649 (p) cc_final: 0.7342 (p) REVERT: J 610 ILE cc_start: 0.8566 (mt) cc_final: 0.8240 (mm) REVERT: A 64 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8326 (mmmm) REVERT: A 106 GLU cc_start: 0.8222 (tp30) cc_final: 0.7936 (tp30) REVERT: A 115 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8686 (ptpp) REVERT: D 556 ASN cc_start: 0.4928 (OUTLIER) cc_final: 0.4425 (p0) REVERT: E 56 HIS cc_start: 0.8423 (m90) cc_final: 0.8109 (m-70) REVERT: E 137 TYR cc_start: 0.7865 (t80) cc_final: 0.7632 (t80) REVERT: E 140 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8675 (mmmt) REVERT: E 142 GLN cc_start: 0.7551 (pm20) cc_final: 0.7138 (pm20) outliers start: 27 outliers final: 22 residues processed: 173 average time/residue: 0.2117 time to fit residues: 51.2850 Evaluate side-chains 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 139 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.162524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107334 restraints weight = 21568.885| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.67 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9798 Z= 0.183 Angle : 0.624 9.021 13364 Z= 0.324 Chirality : 0.044 0.209 1455 Planarity : 0.004 0.041 1742 Dihedral : 4.437 18.929 1301 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.86 % Favored : 91.46 % Rotamer: Outliers : 3.01 % Allowed : 17.30 % Favored : 79.69 % 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: -1.71 (0.23), residues: 1183 helix: -0.02 (0.33), residues: 249 sheet: -0.90 (0.32), residues: 244 loop : -1.68 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.003 0.001 HIS D 510 PHE 0.010 0.001 PHE C 504 TYR 0.009 0.001 TYR C 487 ARG 0.006 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 284) hydrogen bonds : angle 5.10904 ( 762) SS BOND : bond 0.00266 ( 19) SS BOND : angle 0.78556 ( 38) covalent geometry : bond 0.00428 ( 9779) covalent geometry : angle 0.62355 (13326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 547 LEU cc_start: 0.8347 (mt) cc_final: 0.8092 (mt) REVERT: C 569 ASN cc_start: 0.4612 (m-40) cc_final: 0.4304 (m-40) REVERT: I 86 TRP cc_start: 0.8006 (p90) cc_final: 0.7603 (p90) REVERT: I 100 GLU cc_start: 0.8383 (mp0) cc_final: 0.7863 (mp0) REVERT: I 142 GLN cc_start: 0.8114 (pp30) cc_final: 0.7319 (pp30) REVERT: J 551 GLN cc_start: 0.8156 (tt0) cc_final: 0.7825 (mt0) REVERT: J 564 GLU cc_start: 0.8176 (mp0) cc_final: 0.7839 (mp0) REVERT: J 610 ILE cc_start: 0.8578 (mt) cc_final: 0.8236 (mm) REVERT: A 64 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8375 (mmmm) REVERT: A 70 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 106 GLU cc_start: 0.8213 (tp30) cc_final: 0.7922 (tp30) REVERT: A 115 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8717 (ptpp) REVERT: D 556 ASN cc_start: 0.4958 (OUTLIER) cc_final: 0.4445 (p0) outliers start: 31 outliers final: 23 residues processed: 165 average time/residue: 0.2159 time to fit residues: 49.8654 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 544 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 29 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 57 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 GLN I 50 GLN E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.163194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108381 restraints weight = 21479.281| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.70 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9798 Z= 0.113 Angle : 0.604 8.336 13364 Z= 0.314 Chirality : 0.043 0.210 1455 Planarity : 0.004 0.043 1742 Dihedral : 4.339 23.710 1301 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.17 % Favored : 93.24 % Rotamer: Outliers : 1.94 % Allowed : 18.85 % Favored : 79.20 % 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: -1.56 (0.23), residues: 1183 helix: 0.12 (0.34), residues: 247 sheet: -0.80 (0.32), residues: 244 loop : -1.60 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.004 0.000 HIS D 510 PHE 0.008 0.001 PHE C 504 TYR 0.010 0.001 TYR A 162 ARG 0.005 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 284) hydrogen bonds : angle 4.88982 ( 762) SS BOND : bond 0.00307 ( 19) SS BOND : angle 1.04172 ( 38) covalent geometry : bond 0.00250 ( 9779) covalent geometry : angle 0.60219 (13326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 569 ASN cc_start: 0.4748 (m-40) cc_final: 0.4445 (m-40) REVERT: I 86 TRP cc_start: 0.7996 (p90) cc_final: 0.7676 (p90) REVERT: I 100 GLU cc_start: 0.8415 (mp0) cc_final: 0.7951 (mp0) REVERT: I 140 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8876 (tppt) REVERT: I 142 GLN cc_start: 0.8130 (pp30) cc_final: 0.7501 (pp30) REVERT: J 551 GLN cc_start: 0.8087 (tt0) cc_final: 0.7858 (mt0) REVERT: J 564 GLU cc_start: 0.8282 (mp0) cc_final: 0.8026 (mp0) REVERT: J 600 THR cc_start: 0.7834 (p) cc_final: 0.7553 (p) REVERT: J 610 ILE cc_start: 0.8545 (mt) cc_final: 0.8163 (mm) REVERT: A 64 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8443 (mmmm) REVERT: B 545 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: D 556 ASN cc_start: 0.5004 (OUTLIER) cc_final: 0.4491 (p0) REVERT: E 56 HIS cc_start: 0.8441 (m90) cc_final: 0.8137 (m-70) REVERT: E 120 GLU cc_start: 0.7399 (tp30) cc_final: 0.7116 (tp30) REVERT: E 137 TYR cc_start: 0.7856 (t80) cc_final: 0.7654 (t80) outliers start: 20 outliers final: 18 residues processed: 161 average time/residue: 0.2419 time to fit residues: 55.0250 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 30.0000 chunk 62 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 492 HIS ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.164102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108470 restraints weight = 21340.015| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.75 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9798 Z= 0.132 Angle : 0.619 8.539 13364 Z= 0.322 Chirality : 0.044 0.204 1455 Planarity : 0.004 0.043 1742 Dihedral : 4.257 18.924 1301 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.10 % Favored : 92.31 % Rotamer: Outliers : 2.33 % Allowed : 18.08 % Favored : 79.59 % 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: -1.61 (0.23), residues: 1183 helix: 0.02 (0.33), residues: 252 sheet: -0.97 (0.31), residues: 262 loop : -1.55 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.005 0.001 HIS D 510 PHE 0.009 0.001 PHE B 592 TYR 0.010 0.001 TYR I 137 ARG 0.006 0.000 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 284) hydrogen bonds : angle 4.85198 ( 762) SS BOND : bond 0.00239 ( 19) SS BOND : angle 0.91343 ( 38) covalent geometry : bond 0.00306 ( 9779) covalent geometry : angle 0.61802 (13326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4853.65 seconds wall clock time: 84 minutes 39.17 seconds (5079.17 seconds total)