Starting phenix.real_space_refine on Wed Sep 17 15:45:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dz2_47323/09_2025/9dz2_47323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dz2_47323/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dz2_47323/09_2025/9dz2_47323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dz2_47323/09_2025/9dz2_47323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dz2_47323/09_2025/9dz2_47323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dz2_47323/09_2025/9dz2_47323.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.45, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 362.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.31 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: 1.85 Time building geometry restraints manager: 1.19 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG F 602 TYR 0.027 0.002 TYR C 509 PHE 0.022 0.002 PHE C 513 TRP 0.028 0.002 TRP A 86 HIS 0.006 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9779) covalent geometry : angle 0.73915 (13326) SS BOND : bond 0.00428 ( 19) SS BOND : angle 1.79501 ( 38) hydrogen bonds : bond 0.25896 ( 284) hydrogen bonds : angle 9.00938 ( 762) *********************** 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 : 0.369 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: 0.1108 time to fit residues: 35.9638 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 : 0.361 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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** ** I 69 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.167770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113805 restraints weight = 21640.774| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.70 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9798 Z= 0.154 Angle : 0.704 8.337 13364 Z= 0.368 Chirality : 0.045 0.225 1455 Planarity : 0.005 0.047 1742 Dihedral : 5.357 57.352 1303 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.61 % Favored : 91.72 % Rotamer: Outliers : 2.04 % Allowed : 12.15 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.23), residues: 1183 helix: -0.32 (0.33), residues: 230 sheet: -1.09 (0.29), residues: 277 loop : -1.73 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 164 TYR 0.019 0.001 TYR C 555 PHE 0.017 0.002 PHE C 395 TRP 0.015 0.002 TRP A 86 HIS 0.008 0.001 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9779) covalent geometry : angle 0.70309 (13326) SS BOND : bond 0.00314 ( 19) SS BOND : angle 1.09237 ( 38) hydrogen bonds : bond 0.05581 ( 284) hydrogen bonds : angle 6.12441 ( 762) *********************** 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 188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 555 TYR cc_start: 0.8272 (m-80) cc_final: 0.8044 (m-10) REVERT: I 142 GLN cc_start: 0.7576 (pp30) cc_final: 0.7230 (pp30) REVERT: J 551 GLN cc_start: 0.7991 (tt0) cc_final: 0.7732 (mt0) REVERT: A 64 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8211 (mmmm) REVERT: E 142 GLN cc_start: 0.7359 (pm20) cc_final: 0.7110 (pm20) REVERT: E 172 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8092 (ttp80) outliers start: 21 outliers final: 15 residues processed: 176 average time/residue: 0.0954 time to fit residues: 23.8035 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 ILE Chi-restraints excluded: chain A residue 92 VAL 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 E residue 76 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 104 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 478 ASN C 492 HIS ** J 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.163936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108994 restraints weight = 21682.077| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.64 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9798 Z= 0.205 Angle : 0.667 8.865 13364 Z= 0.349 Chirality : 0.046 0.233 1455 Planarity : 0.005 0.051 1742 Dihedral : 5.205 57.930 1303 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.86 % Favored : 91.46 % Rotamer: Outliers : 2.82 % Allowed : 13.80 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.24), residues: 1183 helix: 0.03 (0.35), residues: 224 sheet: -1.04 (0.31), residues: 260 loop : -1.76 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 596 TYR 0.013 0.001 TYR F 582 PHE 0.018 0.002 PHE F 592 TRP 0.018 0.002 TRP A 86 HIS 0.024 0.002 HIS F 524 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9779) covalent geometry : angle 0.66580 (13326) SS BOND : bond 0.00395 ( 19) SS BOND : angle 1.10701 ( 38) hydrogen bonds : bond 0.04674 ( 284) hydrogen bonds : angle 5.73872 ( 762) *********************** 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 182 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7844 (pt) cc_final: 0.7338 (tp) REVERT: C 555 TYR cc_start: 0.8335 (m-80) cc_final: 0.7948 (m-10) REVERT: I 100 GLU cc_start: 0.8258 (mp0) cc_final: 0.7681 (mp0) REVERT: I 142 GLN cc_start: 0.7831 (pp30) cc_final: 0.7385 (pp30) REVERT: J 551 GLN cc_start: 0.8080 (tt0) cc_final: 0.7747 (mt0) REVERT: A 64 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8231 (mmmm) REVERT: A 115 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8661 (ptpp) REVERT: D 514 LEU cc_start: 0.7159 (mt) cc_final: 0.6872 (mt) REVERT: E 120 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 142 GLN cc_start: 0.7485 (pm20) cc_final: 0.7215 (pm20) REVERT: F 544 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8260 (p) outliers start: 29 outliers final: 18 residues processed: 170 average time/residue: 0.0969 time to fit residues: 23.2918 Evaluate side-chains 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 544 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** J 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN B 549 HIS E 56 HIS ** E 142 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 = 0.4243 r_free = 0.4243 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108725 restraints weight = 21910.954| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.71 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9798 Z= 0.209 Angle : 0.647 7.056 13364 Z= 0.341 Chirality : 0.045 0.225 1455 Planarity : 0.005 0.044 1742 Dihedral : 5.066 52.760 1303 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.35 % Favored : 91.97 % Rotamer: Outliers : 2.82 % Allowed : 14.29 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.23), residues: 1183 helix: 0.20 (0.35), residues: 226 sheet: -1.07 (0.31), residues: 256 loop : -1.81 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 164 TYR 0.012 0.001 TYR F 582 PHE 0.011 0.002 PHE C 504 TRP 0.018 0.002 TRP A 86 HIS 0.013 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 9779) covalent geometry : angle 0.64627 (13326) SS BOND : bond 0.00314 ( 19) SS BOND : angle 0.98320 ( 38) hydrogen bonds : bond 0.04213 ( 284) hydrogen bonds : angle 5.52956 ( 762) *********************** 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 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7893 (pt) cc_final: 0.7385 (tp) REVERT: C 481 ILE cc_start: 0.1934 (mm) cc_final: 0.1364 (mm) REVERT: I 100 GLU cc_start: 0.8325 (mp0) cc_final: 0.7743 (mp0) REVERT: I 142 GLN cc_start: 0.7968 (pp30) cc_final: 0.7225 (pp30) REVERT: J 529 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (tp) REVERT: J 551 GLN cc_start: 0.8064 (tt0) cc_final: 0.7766 (mt0) REVERT: A 64 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8306 (mmmm) REVERT: A 115 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8716 (ptpp) REVERT: D 514 LEU cc_start: 0.7245 (mt) cc_final: 0.6968 (mt) REVERT: E 142 GLN cc_start: 0.7576 (pm20) cc_final: 0.7309 (pm20) REVERT: F 544 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8292 (p) outliers start: 29 outliers final: 21 residues processed: 172 average time/residue: 0.0946 time to fit residues: 23.1042 Evaluate side-chains 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 119 SER Chi-restraints excluded: chain I residue 127 ASP 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 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 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS I 62 GLN I 107 ASN J 514 ASN J 549 HIS E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.164268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108873 restraints weight = 21527.577| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.62 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9798 Z= 0.127 Angle : 0.603 8.016 13364 Z= 0.316 Chirality : 0.043 0.241 1455 Planarity : 0.004 0.039 1742 Dihedral : 4.881 50.600 1303 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.10 % Favored : 92.22 % Rotamer: Outliers : 2.92 % Allowed : 15.74 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.23), residues: 1183 helix: 0.03 (0.34), residues: 240 sheet: -0.85 (0.31), residues: 244 loop : -1.77 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 587 TYR 0.010 0.001 TYR C 487 PHE 0.009 0.001 PHE B 592 TRP 0.013 0.001 TRP A 86 HIS 0.014 0.001 HIS F 524 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9779) covalent geometry : angle 0.60153 (13326) SS BOND : bond 0.00354 ( 19) SS BOND : angle 1.08003 ( 38) hydrogen bonds : bond 0.03721 ( 284) hydrogen bonds : angle 5.28671 ( 762) *********************** 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 191 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7928 (pt) cc_final: 0.7416 (tp) REVERT: C 481 ILE cc_start: 0.1830 (mm) cc_final: 0.1370 (mm) REVERT: I 100 GLU cc_start: 0.8374 (mp0) cc_final: 0.7813 (mp0) REVERT: I 140 LYS cc_start: 0.9190 (tppt) cc_final: 0.8872 (mptt) REVERT: I 142 GLN cc_start: 0.8008 (pp30) cc_final: 0.7304 (pp30) REVERT: J 551 GLN cc_start: 0.8119 (tt0) cc_final: 0.7833 (mt0) REVERT: A 64 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8319 (mmmm) REVERT: A 115 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8673 (ptpp) REVERT: B 603 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8188 (tp) REVERT: D 514 LEU cc_start: 0.7298 (mt) cc_final: 0.7033 (mt) REVERT: E 142 GLN cc_start: 0.7662 (pm20) cc_final: 0.7301 (pm20) REVERT: F 544 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8322 (p) outliers start: 30 outliers final: 20 residues processed: 178 average time/residue: 0.0995 time to fit residues: 24.6720 Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 VAL 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 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 90 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 0.0170 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS B 613 HIS E 56 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.165705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110806 restraints weight = 21592.065| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.71 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9798 Z= 0.113 Angle : 0.584 7.699 13364 Z= 0.306 Chirality : 0.043 0.217 1455 Planarity : 0.004 0.040 1742 Dihedral : 4.597 48.229 1303 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.76 % Favored : 92.56 % Rotamer: Outliers : 2.72 % Allowed : 17.10 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.23), residues: 1183 helix: 0.04 (0.33), residues: 246 sheet: -0.81 (0.31), residues: 251 loop : -1.72 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 172 TYR 0.009 0.001 TYR A 162 PHE 0.009 0.001 PHE B 592 TRP 0.012 0.001 TRP A 86 HIS 0.004 0.001 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9779) covalent geometry : angle 0.58312 (13326) SS BOND : bond 0.00170 ( 19) SS BOND : angle 0.85886 ( 38) hydrogen bonds : bond 0.03441 ( 284) hydrogen bonds : angle 5.02198 ( 762) *********************** 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 188 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 ILE cc_start: 0.7946 (pt) cc_final: 0.7428 (tp) REVERT: C 481 ILE cc_start: 0.1867 (mm) cc_final: 0.1463 (mm) REVERT: C 499 LYS cc_start: 0.8741 (tptt) cc_final: 0.8504 (tptt) REVERT: C 569 ASN cc_start: 0.4580 (m-40) cc_final: 0.4288 (m-40) REVERT: I 50 GLN cc_start: 0.9144 (tt0) cc_final: 0.8776 (tt0) REVERT: I 100 GLU cc_start: 0.8373 (mp0) cc_final: 0.7862 (mp0) REVERT: I 142 GLN cc_start: 0.8094 (pp30) cc_final: 0.7461 (pp30) REVERT: J 551 GLN cc_start: 0.8054 (tt0) cc_final: 0.7814 (mt0) REVERT: J 564 GLU cc_start: 0.8306 (mp0) cc_final: 0.7955 (mp0) REVERT: J 610 ILE cc_start: 0.8501 (mt) cc_final: 0.8192 (mm) REVERT: A 33 MET cc_start: 0.6841 (mmm) cc_final: 0.6146 (mmp) REVERT: A 64 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8325 (mmmm) REVERT: B 603 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8053 (tp) REVERT: E 140 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8705 (mmmt) REVERT: E 142 GLN cc_start: 0.7681 (pm20) cc_final: 0.7323 (pm20) outliers start: 28 outliers final: 22 residues processed: 173 average time/residue: 0.1004 time to fit residues: 24.4519 Evaluate side-chains 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain D residue 504 PHE 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 E residue 172 ARG Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4234 r_free = 0.4234 target = 0.162664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106393 restraints weight = 21943.360| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.82 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3836 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= 0.163 Angle : 0.612 7.879 13364 Z= 0.321 Chirality : 0.044 0.220 1455 Planarity : 0.004 0.042 1742 Dihedral : 4.453 22.592 1301 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.27 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 16.52 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.23), residues: 1183 helix: 0.08 (0.33), residues: 246 sheet: -0.77 (0.32), residues: 241 loop : -1.68 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 587 TYR 0.009 0.001 TYR C 487 PHE 0.010 0.001 PHE C 504 TRP 0.015 0.001 TRP A 86 HIS 0.012 0.001 HIS F 524 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9779) covalent geometry : angle 0.61063 (13326) SS BOND : bond 0.00241 ( 19) SS BOND : angle 1.01196 ( 38) hydrogen bonds : bond 0.03554 ( 284) hydrogen bonds : angle 5.03736 ( 762) *********************** 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1925 (mm) cc_final: 0.1542 (mm) REVERT: C 569 ASN cc_start: 0.4578 (m-40) cc_final: 0.4293 (m-40) REVERT: I 100 GLU cc_start: 0.8377 (mp0) cc_final: 0.7892 (mp0) REVERT: I 142 GLN cc_start: 0.8111 (pp30) cc_final: 0.7406 (pp30) REVERT: J 551 GLN cc_start: 0.8100 (tt0) cc_final: 0.7828 (mt0) REVERT: J 610 ILE cc_start: 0.8565 (mt) cc_final: 0.8251 (mm) REVERT: A 64 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8442 (mmmm) REVERT: D 556 ASN cc_start: 0.4860 (OUTLIER) cc_final: 0.4368 (p0) REVERT: E 142 GLN cc_start: 0.7697 (pm20) cc_final: 0.7309 (pm20) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.1015 time to fit residues: 23.2861 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 556 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 544 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 545 GLU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 172 ARG 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 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 HIS ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN F 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.163253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106921 restraints weight = 21994.176| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.84 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9798 Z= 0.136 Angle : 0.596 6.969 13364 Z= 0.312 Chirality : 0.043 0.211 1455 Planarity : 0.004 0.040 1742 Dihedral : 4.355 19.713 1301 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.68 % Favored : 92.65 % Rotamer: Outliers : 2.82 % Allowed : 17.59 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.23), residues: 1183 helix: 0.11 (0.33), residues: 247 sheet: -0.92 (0.31), residues: 259 loop : -1.62 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 587 TYR 0.009 0.001 TYR C 487 PHE 0.035 0.001 PHE F 592 TRP 0.017 0.001 TRP A 86 HIS 0.005 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9779) covalent geometry : angle 0.59514 (13326) SS BOND : bond 0.00271 ( 19) SS BOND : angle 0.75107 ( 38) hydrogen bonds : bond 0.03343 ( 284) hydrogen bonds : angle 4.95628 ( 762) *********************** 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.2028 (mm) cc_final: 0.1648 (mm) REVERT: C 569 ASN cc_start: 0.4591 (m-40) cc_final: 0.4300 (m-40) REVERT: I 100 GLU cc_start: 0.8411 (mp0) cc_final: 0.7938 (mp0) REVERT: I 142 GLN cc_start: 0.8134 (pp30) cc_final: 0.7531 (pp30) REVERT: J 551 GLN cc_start: 0.8136 (tt0) cc_final: 0.7916 (mt0) REVERT: J 564 GLU cc_start: 0.8267 (mp0) cc_final: 0.7993 (mp0) REVERT: J 610 ILE cc_start: 0.8573 (mt) cc_final: 0.8223 (mm) REVERT: A 64 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8451 (mmmm) REVERT: A 115 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8711 (ptpp) REVERT: D 514 LEU cc_start: 0.7311 (mt) cc_final: 0.6936 (mt) REVERT: D 556 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4319 (p0) REVERT: E 142 GLN cc_start: 0.7683 (pm20) cc_final: 0.7252 (pm20) outliers start: 29 outliers final: 26 residues processed: 166 average time/residue: 0.1017 time to fit residues: 23.7496 Evaluate side-chains 168 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 556 ASN Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain J residue 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 E residue 172 ARG Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 610 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 32 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 98 optimal weight: 0.0970 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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** I 50 GLN I 139 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.164606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109964 restraints weight = 21348.252| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.68 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9798 Z= 0.110 Angle : 0.586 7.505 13364 Z= 0.305 Chirality : 0.043 0.218 1455 Planarity : 0.004 0.042 1742 Dihedral : 4.176 19.428 1301 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.09 % Favored : 93.24 % Rotamer: Outliers : 2.04 % Allowed : 18.37 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.23), residues: 1183 helix: 0.38 (0.34), residues: 241 sheet: -0.79 (0.32), residues: 260 loop : -1.56 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 587 TYR 0.009 0.001 TYR C 487 PHE 0.028 0.001 PHE F 592 TRP 0.016 0.001 TRP A 86 HIS 0.003 0.000 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9779) covalent geometry : angle 0.58515 (13326) SS BOND : bond 0.00162 ( 19) SS BOND : angle 0.71702 ( 38) hydrogen bonds : bond 0.03121 ( 284) hydrogen bonds : angle 4.74141 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 481 ILE cc_start: 0.1949 (mm) cc_final: 0.1580 (mm) REVERT: C 569 ASN cc_start: 0.4620 (m-40) cc_final: 0.4323 (m-40) REVERT: I 50 GLN cc_start: 0.9255 (pt0) cc_final: 0.9022 (pt0) REVERT: I 100 GLU cc_start: 0.8452 (mp0) cc_final: 0.8004 (mp0) REVERT: I 142 GLN cc_start: 0.8098 (pp30) cc_final: 0.7672 (pp30) REVERT: J 564 GLU cc_start: 0.8309 (mp0) cc_final: 0.8082 (mp0) REVERT: J 610 ILE cc_start: 0.8627 (mt) cc_final: 0.8258 (mm) REVERT: A 64 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8455 (mmmm) REVERT: A 115 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8623 (ptpp) REVERT: B 545 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 514 LEU cc_start: 0.7459 (mt) cc_final: 0.7087 (mt) REVERT: D 556 ASN cc_start: 0.4892 (OUTLIER) cc_final: 0.4356 (p0) REVERT: E 142 GLN cc_start: 0.7765 (pm20) cc_final: 0.7260 (pm20) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.0999 time to fit residues: 23.0516 Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 119 SER Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 172 ARG 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 102 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** J 551 GLN A 50 GLN ** 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 = 0.4246 r_free = 0.4246 target = 0.163974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107399 restraints weight = 21624.351| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.87 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4290 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 : 0.600 7.921 13364 Z= 0.314 Chirality : 0.044 0.205 1455 Planarity : 0.004 0.043 1742 Dihedral : 4.229 18.820 1301 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.93 % Favored : 92.48 % Rotamer: Outliers : 1.85 % Allowed : 19.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.24), residues: 1183 helix: 0.33 (0.34), residues: 243 sheet: -0.85 (0.31), residues: 262 loop : -1.50 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 587 TYR 0.013 0.001 TYR E 137 PHE 0.027 0.001 PHE F 592 TRP 0.018 0.001 TRP A 86 HIS 0.004 0.001 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9779) covalent geometry : angle 0.59923 (13326) SS BOND : bond 0.00227 ( 19) SS BOND : angle 0.78180 ( 38) hydrogen bonds : bond 0.03193 ( 284) hydrogen bonds : angle 4.78175 ( 762) ********************** 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 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 569 ASN cc_start: 0.4789 (m-40) cc_final: 0.4487 (m-40) REVERT: I 100 GLU cc_start: 0.8430 (mp0) cc_final: 0.7963 (mp0) REVERT: I 142 GLN cc_start: 0.8147 (pp30) cc_final: 0.7630 (pp30) REVERT: J 564 GLU cc_start: 0.8288 (mp0) cc_final: 0.8045 (mp0) REVERT: J 610 ILE cc_start: 0.8503 (mt) cc_final: 0.8223 (mm) REVERT: A 64 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8423 (mmmm) REVERT: A 114 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8542 (ptpt) REVERT: B 545 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: D 514 LEU cc_start: 0.7487 (mt) cc_final: 0.7119 (mt) REVERT: D 556 ASN cc_start: 0.4888 (OUTLIER) cc_final: 0.4355 (p0) REVERT: E 142 GLN cc_start: 0.7716 (pm20) cc_final: 0.7223 (pm20) outliers start: 19 outliers final: 17 residues processed: 155 average time/residue: 0.1047 time to fit residues: 22.4917 Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 119 SER Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 172 ARG 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 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 30 optimal weight: 0.0070 chunk 89 optimal weight: 50.0000 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 61 optimal weight: 0.1980 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 overall best weight: 0.1798 ------------------------------------------------------------------------------- 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** I 50 GLN ** 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 = 0.4273 r_free = 0.4273 target = 0.165594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109481 restraints weight = 21564.662| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.84 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9798 Z= 0.110 Angle : 0.585 7.611 13364 Z= 0.307 Chirality : 0.043 0.250 1455 Planarity : 0.004 0.043 1742 Dihedral : 4.107 18.821 1301 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.58 % Favored : 93.83 % Rotamer: Outliers : 2.14 % Allowed : 18.56 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.24), residues: 1183 helix: 0.46 (0.34), residues: 242 sheet: -0.74 (0.32), residues: 251 loop : -1.46 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 587 TYR 0.014 0.001 TYR E 137 PHE 0.028 0.001 PHE F 592 TRP 0.017 0.001 TRP A 86 HIS 0.003 0.000 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9779) covalent geometry : angle 0.58449 (13326) SS BOND : bond 0.00155 ( 19) SS BOND : angle 0.72380 ( 38) hydrogen bonds : bond 0.02951 ( 284) hydrogen bonds : angle 4.58286 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.91 seconds wall clock time: 43 minutes 37.88 seconds (2617.88 seconds total)