Starting phenix.real_space_refine on Wed Apr 30 11:47:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dz2_47323/04_2025/9dz2_47323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dz2_47323/04_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_47323/04_2025/9dz2_47323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dz2_47323/04_2025/9dz2_47323.map" model { file = "/net/cci-nas-00/data/ceres_data/9dz2_47323/04_2025/9dz2_47323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dz2_47323/04_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-5669/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: 6.38, 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 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: 1.19 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: 2.48 Time building geometry restraints manager: 2.71 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: 2.260 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 24.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- 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 : 1.270 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: 0.2669 time to fit residues: 86.7803 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 : 1.187 ------------------------------------------------------------------------------- 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 = 0.110978 restraints weight = 21614.675| |-----------------------------------------------------------------------------| 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 : 0.983 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: 0.8306 (m-80) cc_final: 0.8005 (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: 0.8211 (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: 0.2044 time to fit residues: 49.8653 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 : 0.950 ------------------------------------------------------------------------------- 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: 1.9990 chunk 116 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.164885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108651 restraints weight = 22023.482| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.77 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9798 Z= 0.174 Angle : 0.638 7.147 13364 Z= 0.336 Chirality : 0.045 0.241 1455 Planarity : 0.004 0.045 1742 Dihedral : 5.128 57.257 1303 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.61 % Favored : 91.72 % Rotamer: Outliers : 2.53 % Allowed : 14.19 % Favored : 83.28 % 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: -1.83 (0.24), residues: 1183 helix: 0.00 (0.35), residues: 226 sheet: -1.09 (0.30), residues: 278 loop : -1.73 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.018 0.001 HIS F 524 PHE 0.018 0.002 PHE F 592 TYR 0.012 0.001 TYR F 582 ARG 0.004 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 284) hydrogen bonds : angle 5.64772 ( 762) SS BOND : bond 0.00335 ( 19) SS BOND : angle 1.04145 ( 38) covalent geometry : bond 0.00404 ( 9779) covalent geometry : angle 0.63694 (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 : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7845 (pt) cc_final: 0.7329 (tp) REVERT: I 100 GLU cc_start: 0.8282 (mp0) cc_final: 0.7715 (mp0) REVERT: I 140 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8902 (mmtm) REVERT: I 142 GLN cc_start: 0.7838 (pp30) cc_final: 0.7392 (pp30) REVERT: J 551 GLN cc_start: 0.8045 (tt0) cc_final: 0.7715 (mt0) REVERT: A 64 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8217 (mmmm) REVERT: B 549 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8260 (t-90) REVERT: D 514 LEU cc_start: 0.7191 (mt) cc_final: 0.6907 (mt) REVERT: E 120 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7775 (mt-10) REVERT: E 142 GLN cc_start: 0.7539 (pm20) cc_final: 0.7298 (pm20) REVERT: F 544 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8241 (p) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.2263 time to fit residues: 53.9944 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 : 1.239 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- 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** I 62 GLN ** B 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109275 restraints weight = 21637.877| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.70 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3171 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= 0.187 Angle : 0.629 7.025 13364 Z= 0.331 Chirality : 0.045 0.245 1455 Planarity : 0.004 0.041 1742 Dihedral : 5.000 52.928 1303 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.19 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 14.29 % Favored : 82.99 % 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: -1.80 (0.23), residues: 1183 helix: 0.20 (0.35), residues: 226 sheet: -1.07 (0.31), residues: 258 loop : -1.78 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.008 0.001 HIS C 492 PHE 0.012 0.001 PHE C 542 TYR 0.013 0.001 TYR C 555 ARG 0.004 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 284) hydrogen bonds : angle 5.51723 ( 762) SS BOND : bond 0.00247 ( 19) SS BOND : angle 0.96391 ( 38) covalent geometry : bond 0.00433 ( 9779) covalent geometry : angle 0.62760 (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 183 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7898 (pt) cc_final: 0.7389 (tp) REVERT: C 481 ILE cc_start: 0.1936 (mm) cc_final: 0.1359 (mm) REVERT: C 492 HIS cc_start: 0.8175 (t-90) cc_final: 0.7947 (t-90) REVERT: I 50 GLN cc_start: 0.8969 (tt0) cc_final: 0.8733 (tt0) REVERT: I 100 GLU cc_start: 0.8328 (mp0) cc_final: 0.7741 (mp0) REVERT: I 140 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8926 (mmtm) REVERT: I 142 GLN cc_start: 0.7957 (pp30) cc_final: 0.7193 (pp30) REVERT: J 529 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8645 (tp) REVERT: J 551 GLN cc_start: 0.8041 (tt0) cc_final: 0.7765 (mt0) REVERT: A 64 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8269 (mmmm) REVERT: A 115 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8671 (ptpp) REVERT: B 549 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: D 514 LEU cc_start: 0.7264 (mt) cc_final: 0.6991 (mt) REVERT: E 56 HIS cc_start: 0.8293 (m-70) cc_final: 0.8036 (m90) REVERT: E 142 GLN cc_start: 0.7605 (pm20) cc_final: 0.7350 (pm20) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.2032 time to fit residues: 49.6545 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 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 549 HIS 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: 0.7980 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** I 107 ASN 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 523 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 = 0.4254 r_free = 0.4254 target = 0.164354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109069 restraints weight = 21692.496| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.72 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3430 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= 0.162 Angle : 0.613 7.730 13364 Z= 0.322 Chirality : 0.044 0.236 1455 Planarity : 0.004 0.039 1742 Dihedral : 4.901 49.793 1303 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.27 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 15.16 % Favored : 81.73 % 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: 0.04 (0.34), residues: 240 sheet: -1.00 (0.31), residues: 253 loop : -1.75 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.018 0.001 HIS F 524 PHE 0.010 0.001 PHE C 504 TYR 0.012 0.001 TYR C 555 ARG 0.004 0.000 ARG B 596 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 284) hydrogen bonds : angle 5.34179 ( 762) SS BOND : bond 0.00311 ( 19) SS BOND : angle 1.09435 ( 38) covalent geometry : bond 0.00377 ( 9779) covalent geometry : angle 0.61156 (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 193 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7974 (pt) cc_final: 0.7471 (tp) REVERT: C 481 ILE cc_start: 0.1830 (mm) cc_final: 0.1531 (mm) REVERT: C 492 HIS cc_start: 0.7957 (t-90) cc_final: 0.7591 (t-90) REVERT: I 50 GLN cc_start: 0.9001 (tt0) cc_final: 0.8763 (tt0) REVERT: I 100 GLU cc_start: 0.8337 (mp0) cc_final: 0.7790 (mp0) REVERT: I 140 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8950 (mmtm) REVERT: I 142 GLN cc_start: 0.8003 (pp30) cc_final: 0.7220 (pp30) REVERT: J 551 GLN cc_start: 0.8087 (tt0) cc_final: 0.7822 (mt0) REVERT: A 64 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8298 (mmmm) REVERT: B 603 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8176 (tp) REVERT: D 514 LEU cc_start: 0.7308 (mt) cc_final: 0.7043 (mt) REVERT: E 112 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7518 (tm-30) REVERT: E 114 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8072 (mttm) REVERT: E 142 GLN cc_start: 0.7638 (pm20) cc_final: 0.7281 (pm20) REVERT: E 172 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8222 (ttp80) outliers start: 32 outliers final: 23 residues processed: 181 average time/residue: 0.2164 time to fit residues: 54.5067 Evaluate side-chains 178 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 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 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: 9.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 63 optimal weight: 0.0170 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.163283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107304 restraints weight = 21654.972| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.67 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3701 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= 0.155 Angle : 0.599 7.456 13364 Z= 0.314 Chirality : 0.044 0.227 1455 Planarity : 0.004 0.038 1742 Dihedral : 4.528 19.865 1301 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.27 % Favored : 92.05 % Rotamer: Outliers : 2.82 % Allowed : 17.20 % Favored : 79.98 % 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: -1.75 (0.23), residues: 1183 helix: -0.07 (0.33), residues: 248 sheet: -0.83 (0.32), residues: 244 loop : -1.75 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 86 HIS 0.004 0.001 HIS D 510 PHE 0.010 0.001 PHE C 504 TYR 0.010 0.001 TYR C 487 ARG 0.003 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 284) hydrogen bonds : angle 5.18607 ( 762) SS BOND : bond 0.00227 ( 19) SS BOND : angle 0.89838 ( 38) covalent geometry : bond 0.00361 ( 9779) covalent geometry : angle 0.59811 (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 187 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1786 (mm) cc_final: 0.1399 (mm) REVERT: C 569 ASN cc_start: 0.4550 (m-40) cc_final: 0.4281 (m-40) REVERT: I 86 TRP cc_start: 0.7954 (p90) cc_final: 0.7631 (p90) REVERT: I 100 GLU cc_start: 0.8401 (mp0) cc_final: 0.7872 (mp0) REVERT: I 140 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8957 (mmtm) REVERT: I 142 GLN cc_start: 0.8065 (pp30) cc_final: 0.7272 (pp30) REVERT: J 551 GLN cc_start: 0.8102 (tt0) cc_final: 0.7844 (mt0) REVERT: J 600 THR cc_start: 0.7671 (p) cc_final: 0.7275 (p) REVERT: J 610 ILE cc_start: 0.8541 (mt) cc_final: 0.8211 (mm) REVERT: A 64 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8342 (mmmm) REVERT: D 514 LEU cc_start: 0.7282 (mt) cc_final: 0.7001 (mt) REVERT: E 56 HIS cc_start: 0.8392 (m90) cc_final: 0.8012 (m90) REVERT: E 142 GLN cc_start: 0.7639 (pm20) cc_final: 0.7211 (pm20) REVERT: E 172 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7935 (ttp80) REVERT: F 521 GLN cc_start: 0.7450 (pp30) cc_final: 0.7242 (pp30) outliers start: 29 outliers final: 25 residues processed: 176 average time/residue: 0.2430 time to fit residues: 59.9001 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 : 1.088 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.4980 chunk 110 optimal weight: 0.0870 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 50.0000 chunk 84 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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** I 175 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.164668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109425 restraints weight = 21789.557| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.76 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3830 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= 0.135 Angle : 0.598 8.289 13364 Z= 0.313 Chirality : 0.043 0.220 1455 Planarity : 0.004 0.038 1742 Dihedral : 4.463 20.528 1301 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.52 % Favored : 91.80 % Rotamer: Outliers : 3.21 % Allowed : 17.01 % Favored : 79.79 % 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 : -1.70 (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 F 524 PHE 0.009 0.001 PHE C 504 TYR 0.009 0.001 TYR C 487 ARG 0.007 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 284) hydrogen bonds : angle 5.07115 ( 762) SS BOND : bond 0.00300 ( 19) SS BOND : angle 1.09562 ( 38) covalent geometry : bond 0.00310 ( 9779) covalent geometry : angle 0.59596 (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: 33 poor density : 156 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1787 (mm) cc_final: 0.1403 (mm) REVERT: C 569 ASN cc_start: 0.4551 (m-40) cc_final: 0.4265 (m-40) REVERT: I 86 TRP cc_start: 0.7953 (p90) cc_final: 0.7596 (p90) REVERT: I 100 GLU cc_start: 0.8406 (mp0) cc_final: 0.7880 (mp0) REVERT: I 140 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8950 (mmtm) REVERT: I 142 GLN cc_start: 0.8082 (pp30) cc_final: 0.7316 (pp30) REVERT: J 551 GLN cc_start: 0.8067 (tt0) cc_final: 0.7807 (mt0) REVERT: J 564 GLU cc_start: 0.8207 (mp0) cc_final: 0.7848 (mp0) REVERT: J 610 ILE cc_start: 0.8565 (mt) cc_final: 0.8188 (mm) REVERT: A 64 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8358 (mmmm) REVERT: D 514 LEU cc_start: 0.7305 (mt) cc_final: 0.6912 (mt) REVERT: D 556 ASN cc_start: 0.4880 (OUTLIER) cc_final: 0.4359 (p0) REVERT: E 140 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8706 (mmmt) REVERT: E 142 GLN cc_start: 0.7628 (pm20) cc_final: 0.7246 (pm20) REVERT: E 172 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7950 (ttp80) outliers start: 33 outliers final: 25 residues processed: 179 average time/residue: 0.2807 time to fit residues: 71.1109 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 A residue 39 THR Chi-restraints excluded: chain A residue 52 VAL 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 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: 10.0000 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.161152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105007 restraints weight = 22105.027| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.74 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9798 Z= 0.235 Angle : 0.658 6.678 13364 Z= 0.343 Chirality : 0.046 0.212 1455 Planarity : 0.005 0.041 1742 Dihedral : 4.686 19.168 1301 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.69 % Favored : 91.63 % Rotamer: Outliers : 3.11 % Allowed : 17.78 % Favored : 79.11 % 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: -1.81 (0.23), residues: 1183 helix: 0.07 (0.34), residues: 243 sheet: -1.07 (0.32), residues: 246 loop : -1.78 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 86 HIS 0.004 0.001 HIS D 510 PHE 0.033 0.002 PHE F 592 TYR 0.013 0.001 TYR C 487 ARG 0.006 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 284) hydrogen bonds : angle 5.28258 ( 762) SS BOND : bond 0.00295 ( 19) SS BOND : angle 0.95871 ( 38) covalent geometry : bond 0.00555 ( 9779) covalent geometry : angle 0.65668 (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 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 547 LEU cc_start: 0.8371 (mt) cc_final: 0.8109 (mt) REVERT: C 569 ASN cc_start: 0.4640 (m-40) cc_final: 0.4348 (m-40) REVERT: I 50 GLN cc_start: 0.9107 (tt0) cc_final: 0.8875 (pt0) REVERT: I 100 GLU cc_start: 0.8379 (mp0) cc_final: 0.7855 (mp0) REVERT: I 140 LYS cc_start: 0.9313 (mmmm) cc_final: 0.9003 (mmtm) REVERT: I 142 GLN cc_start: 0.8124 (pp30) cc_final: 0.7557 (pp30) REVERT: J 551 GLN cc_start: 0.8164 (tt0) cc_final: 0.7827 (mt0) REVERT: J 600 THR cc_start: 0.7798 (p) cc_final: 0.7535 (p) REVERT: J 610 ILE cc_start: 0.8606 (mt) cc_final: 0.8227 (mm) REVERT: A 64 LYS cc_start: 0.8712 (mmmm) cc_final: 0.8373 (mmmm) REVERT: A 70 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 115 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8738 (ptpp) REVERT: D 514 LEU cc_start: 0.7412 (mt) cc_final: 0.7037 (mt) REVERT: D 556 ASN cc_start: 0.4888 (OUTLIER) cc_final: 0.4355 (p0) REVERT: E 56 HIS cc_start: 0.8439 (m90) cc_final: 0.8147 (m-70) REVERT: E 142 GLN cc_start: 0.7660 (pm20) cc_final: 0.7252 (pm20) outliers start: 32 outliers final: 26 residues processed: 165 average time/residue: 0.2922 time to fit residues: 68.0393 Evaluate side-chains 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 127 ASP 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 544 THR 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 60 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 565 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: 7.9990 chunk 108 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 GLN ** C 510 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.162423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107262 restraints weight = 21643.603| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.71 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9798 Z= 0.158 Angle : 0.617 6.960 13364 Z= 0.322 Chirality : 0.044 0.218 1455 Planarity : 0.004 0.042 1742 Dihedral : 4.538 18.865 1301 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.93 % Favored : 92.39 % Rotamer: Outliers : 2.72 % Allowed : 18.17 % Favored : 79.11 % 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: -0.01 (0.33), residues: 249 sheet: -1.05 (0.32), residues: 247 loop : -1.71 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 86 HIS 0.003 0.001 HIS D 510 PHE 0.030 0.001 PHE F 592 TYR 0.011 0.001 TYR I 137 ARG 0.005 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 284) hydrogen bonds : angle 5.11382 ( 762) SS BOND : bond 0.00206 ( 19) SS BOND : angle 0.78019 ( 38) covalent geometry : bond 0.00371 ( 9779) covalent geometry : angle 0.61628 (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 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: C 547 LEU cc_start: 0.8419 (mt) cc_final: 0.8139 (mt) REVERT: C 569 ASN cc_start: 0.4615 (m-40) cc_final: 0.4299 (m-40) REVERT: I 100 GLU cc_start: 0.8433 (mp0) cc_final: 0.7919 (mp0) REVERT: I 140 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9000 (mmtm) REVERT: I 142 GLN cc_start: 0.8186 (pp30) cc_final: 0.7396 (pp30) REVERT: J 551 GLN cc_start: 0.8111 (tt0) cc_final: 0.7821 (mt0) REVERT: J 564 GLU cc_start: 0.8188 (mp0) cc_final: 0.7900 (mp0) REVERT: J 610 ILE cc_start: 0.8584 (mt) cc_final: 0.8205 (mm) REVERT: A 64 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8364 (mmmm) REVERT: A 70 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 115 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8728 (ptpp) REVERT: D 514 LEU cc_start: 0.7407 (mt) cc_final: 0.7031 (mt) REVERT: D 556 ASN cc_start: 0.4925 (OUTLIER) cc_final: 0.4383 (p0) REVERT: E 142 GLN cc_start: 0.7676 (pm20) cc_final: 0.7186 (pm20) outliers start: 28 outliers final: 26 residues processed: 163 average time/residue: 0.2251 time to fit residues: 51.0591 Evaluate side-chains 168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 127 ASP 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 544 THR 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 60 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 565 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: 0.0010 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 64 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 overall best weight: 0.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 139 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.163208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107007 restraints weight = 21991.189| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.85 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4359 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 : 0.593 7.389 13364 Z= 0.308 Chirality : 0.043 0.217 1455 Planarity : 0.004 0.044 1742 Dihedral : 4.335 19.212 1301 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.93 % Favored : 92.39 % Rotamer: Outliers : 2.14 % Allowed : 18.37 % Favored : 79.49 % 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: -1.57 (0.23), residues: 1183 helix: 0.29 (0.34), residues: 241 sheet: -1.03 (0.33), residues: 234 loop : -1.57 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 86 HIS 0.003 0.000 HIS D 510 PHE 0.030 0.001 PHE F 592 TYR 0.009 0.001 TYR C 509 ARG 0.005 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 284) hydrogen bonds : angle 4.86252 ( 762) SS BOND : bond 0.00173 ( 19) SS BOND : angle 0.74347 ( 38) covalent geometry : bond 0.00266 ( 9779) covalent geometry : angle 0.59202 (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 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 547 LEU cc_start: 0.8427 (mt) cc_final: 0.8141 (mt) REVERT: C 569 ASN cc_start: 0.4769 (m-40) cc_final: 0.4450 (m-40) REVERT: I 100 GLU cc_start: 0.8453 (mp0) cc_final: 0.8020 (mp0) REVERT: I 142 GLN cc_start: 0.8198 (pp30) cc_final: 0.7513 (pp30) REVERT: J 551 GLN cc_start: 0.8134 (tt0) cc_final: 0.7857 (mt0) REVERT: J 564 GLU cc_start: 0.8275 (mp0) cc_final: 0.8070 (mp0) REVERT: J 610 ILE cc_start: 0.8508 (mt) cc_final: 0.8103 (mm) REVERT: A 64 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8473 (mmmm) REVERT: B 545 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: D 514 LEU cc_start: 0.7437 (mt) cc_final: 0.7068 (mt) REVERT: D 556 ASN cc_start: 0.4825 (OUTLIER) cc_final: 0.4284 (p0) REVERT: E 142 GLN cc_start: 0.7717 (pm20) cc_final: 0.7284 (pm20) outliers start: 22 outliers final: 19 residues processed: 165 average time/residue: 0.2109 time to fit residues: 48.5269 Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 127 ASP Chi-restraints excluded: chain J residue 544 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 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 49 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 8 optimal weight: 50.0000 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.163469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107013 restraints weight = 21722.681| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.86 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9798 Z= 0.129 Angle : 0.623 8.854 13364 Z= 0.324 Chirality : 0.044 0.209 1455 Planarity : 0.004 0.044 1742 Dihedral : 4.286 19.514 1301 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.59 % Favored : 92.81 % Rotamer: Outliers : 2.04 % Allowed : 19.44 % Favored : 78.52 % 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: -1.60 (0.23), residues: 1183 helix: 0.26 (0.34), residues: 243 sheet: -1.08 (0.31), residues: 262 loop : -1.57 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.003 0.000 HIS D 510 PHE 0.029 0.001 PHE F 592 TYR 0.013 0.001 TYR E 137 ARG 0.006 0.000 ARG J 587 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 284) hydrogen bonds : angle 4.83866 ( 762) SS BOND : bond 0.00202 ( 19) SS BOND : angle 0.82818 ( 38) covalent geometry : bond 0.00298 ( 9779) covalent geometry : angle 0.62229 (13326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.05 seconds wall clock time: 89 minutes 24.92 seconds (5364.92 seconds total)