Starting phenix.real_space_refine on Sun May 18 09:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo5_61644/05_2025/9jo5_61644.cif" } resolution = 2.8 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= 0.009 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: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 26 5.16 5 C 9822 2.51 5 N 3120 2.21 5 O 3770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17033 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4946 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.10, per 1000 atoms: 0.59 Number of scatterers: 17033 At special positions: 0 Unit cell: (105.002, 119.075, 155.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 294 15.00 Mg 1 11.99 O 3770 8.00 N 3120 7.00 C 9822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 62.9% alpha, 3.0% beta 135 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 8.28 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.551A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.675A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.661A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.131A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.563A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.686A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.640A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.690A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.963A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.539A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.546A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 91 removed outlier: 3.706A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 115 Processing helix chain 'K' and resid 119 through 130 removed outlier: 3.809A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.914A pdb=" N VAL K 139 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.802A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.691A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 342 removed outlier: 4.121A pdb=" N GLU K 342 " --> pdb=" O GLN K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 378 through 386 Processing helix chain 'K' and resid 390 through 406 removed outlier: 4.103A pdb=" N GLN K 394 " --> pdb=" O THR K 390 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS K 399 " --> pdb=" O ASP K 395 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 409 No H-bonds generated for 'chain 'K' and resid 407 through 409' Processing helix chain 'K' and resid 434 through 448 Processing helix chain 'K' and resid 461 through 478 Processing helix chain 'K' and resid 501 through 518 removed outlier: 4.667A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.625A pdb=" N LEU K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 556 through 565 Processing helix chain 'K' and resid 601 through 610 removed outlier: 3.799A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 654 removed outlier: 4.038A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 636 " --> pdb=" O VAL K 632 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU K 637 " --> pdb=" O GLU K 633 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU K 638 " --> pdb=" O GLU K 634 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN K 648 " --> pdb=" O LEU K 644 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) Processing helix chain 'K' and resid 669 through 676 Processing helix chain 'K' and resid 678 through 685 removed outlier: 3.744A pdb=" N VAL K 682 " --> pdb=" O GLY K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.839A pdb=" N LEU K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.316A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.013A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.731A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.825A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.165A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.637A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 425 through 426 removed outlier: 6.199A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 429 through 431 removed outlier: 6.235A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 524 through 525 588 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 676 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 8.91 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3094 1.33 - 1.45: 5512 1.45 - 1.57: 8696 1.57 - 1.69: 585 1.69 - 1.81: 45 Bond restraints: 17932 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" N THR K 419 " pdb=" CA THR K 419 " ideal model delta sigma weight residual 1.458 1.412 0.046 1.14e-02 7.69e+03 1.66e+01 bond pdb=" CA THR K 419 " pdb=" C THR K 419 " ideal model delta sigma weight residual 1.524 1.474 0.051 1.29e-02 6.01e+03 1.54e+01 bond pdb=" CA SER K 420 " pdb=" C SER K 420 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.93e+00 bond pdb=" N SER K 420 " pdb=" CA SER K 420 " ideal model delta sigma weight residual 1.457 1.425 0.033 1.29e-02 6.01e+03 6.49e+00 ... (remaining 17927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25012 2.38 - 4.77: 418 4.77 - 7.15: 34 7.15 - 9.54: 5 9.54 - 11.92: 1 Bond angle restraints: 25470 Sorted by residual: angle pdb=" N THR K 419 " pdb=" CA THR K 419 " pdb=" C THR K 419 " ideal model delta sigma weight residual 112.41 100.49 11.92 1.30e+00 5.92e-01 8.41e+01 angle pdb=" CA VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 116.60 109.80 6.80 1.45e+00 4.76e-01 2.20e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 108.90 116.04 -7.14 1.63e+00 3.76e-01 1.92e+01 angle pdb=" O VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 122.57 128.04 -5.47 1.25e+00 6.40e-01 1.91e+01 angle pdb=" N ILE K 397 " pdb=" CA ILE K 397 " pdb=" C ILE K 397 " ideal model delta sigma weight residual 112.98 107.79 5.19 1.25e+00 6.40e-01 1.73e+01 ... (remaining 25465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 8570 35.81 - 71.62: 1469 71.62 - 107.43: 37 107.43 - 143.24: 0 143.24 - 179.05: 4 Dihedral angle restraints: 10080 sinusoidal: 6058 harmonic: 4022 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 42.08 -102.08 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" CA PRO K 479 " pdb=" C PRO K 479 " pdb=" N TYR K 480 " pdb=" CA TYR K 480 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT I 38 " pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " pdb=" P DA I 39 " ideal model delta sinusoidal sigma weight residual -140.00 39.05 -179.05 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1913 0.045 - 0.090: 795 0.090 - 0.136: 151 0.136 - 0.181: 19 0.181 - 0.226: 5 Chirality restraints: 2883 Sorted by residual: chirality pdb=" C3' DT I 38 " pdb=" C4' DT I 38 " pdb=" O3' DT I 38 " pdb=" C2' DT I 38 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE H 36 " pdb=" CA ILE H 36 " pdb=" CG1 ILE H 36 " pdb=" CG2 ILE H 36 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR K 352 " pdb=" CA THR K 352 " pdb=" OG1 THR K 352 " pdb=" CG2 THR K 352 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 2880 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 417 " 0.027 2.00e-02 2.50e+03 5.88e-02 3.46e+01 pdb=" C VAL K 417 " -0.102 2.00e-02 2.50e+03 pdb=" O VAL K 417 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU K 418 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.019 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE G 25 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.031 2.00e-02 2.50e+03 1.32e-02 4.81e+00 pdb=" N9 DA I 20 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.003 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 143 2.53 - 3.13: 13213 3.13 - 3.72: 29476 3.72 - 4.31: 41909 4.31 - 4.90: 62129 Nonbonded interactions: 146870 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O3B ADP K1202 " model vdw 1.943 2.170 nonbonded pdb=" N2 DG I 44 " pdb=" O2 DC J 104 " model vdw 1.954 2.496 nonbonded pdb=" O2 DC I 45 " pdb=" N2 DG J 103 " model vdw 1.973 2.496 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.073 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.139 3.040 ... (remaining 146865 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 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 14 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 47.550 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.011 0.076 17932 Z= 0.468 Angle : 0.803 11.919 25470 Z= 0.468 Chirality : 0.048 0.226 2883 Planarity : 0.004 0.059 2222 Dihedral : 26.063 179.048 7476 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1357 helix: 0.79 (0.18), residues: 816 sheet: -2.80 (0.61), residues: 61 loop : -1.79 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 600 HIS 0.004 0.001 HIS F 18 PHE 0.041 0.002 PHE G 25 TYR 0.033 0.002 TYR K 320 ARG 0.011 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.13350 ( 932) hydrogen bonds : angle 4.81266 ( 2404) covalent geometry : bond 0.01051 (17932) covalent geometry : angle 0.80265 (25470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.451 Fit side-chains REVERT: C 90 ASP cc_start: 0.8584 (t0) cc_final: 0.8372 (t0) REVERT: D 65 ASP cc_start: 0.8533 (t70) cc_final: 0.8152 (t0) REVERT: D 73 GLU cc_start: 0.8323 (tp30) cc_final: 0.8101 (tp30) REVERT: D 76 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: H 73 GLU cc_start: 0.8505 (tp30) cc_final: 0.8193 (tp30) REVERT: K 211 HIS cc_start: 0.8391 (t70) cc_final: 0.8178 (t-90) REVERT: K 223 MET cc_start: 0.8601 (ttt) cc_final: 0.8372 (tpp) REVERT: K 294 CYS cc_start: 0.8294 (m) cc_final: 0.8024 (m) REVERT: K 418 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: K 527 MET cc_start: 0.8822 (tmm) cc_final: 0.8389 (tmt) REVERT: K 606 LEU cc_start: 0.9532 (tt) cc_final: 0.9031 (tt) REVERT: K 609 MET cc_start: 0.9477 (ptm) cc_final: 0.8727 (ppp) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 1.9210 time to fit residues: 348.4377 Evaluate side-chains 136 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 418 GLU Chi-restraints excluded: chain K residue 524 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS K 526 GLN ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 586 ASN K 603 GLN K 677 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.098200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066345 restraints weight = 47163.959| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.21 r_work: 0.3061 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17932 Z= 0.170 Angle : 0.626 8.816 25470 Z= 0.355 Chirality : 0.038 0.181 2883 Planarity : 0.004 0.041 2222 Dihedral : 29.220 179.775 4721 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.28 % Allowed : 9.01 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1357 helix: 1.47 (0.18), residues: 834 sheet: -2.72 (0.66), residues: 50 loop : -1.62 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 364 HIS 0.005 0.001 HIS K 111 PHE 0.013 0.001 PHE K 574 TYR 0.018 0.001 TYR K 499 ARG 0.006 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 932) hydrogen bonds : angle 3.54660 ( 2404) covalent geometry : bond 0.00370 (17932) covalent geometry : angle 0.62575 (25470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9208 (ttpt) REVERT: D 65 ASP cc_start: 0.8804 (t70) cc_final: 0.8294 (t0) REVERT: D 90 GLU cc_start: 0.8945 (mp0) cc_final: 0.8679 (mp0) REVERT: F 95 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7586 (mtp85) REVERT: G 90 ASP cc_start: 0.9042 (t0) cc_final: 0.8828 (t0) REVERT: H 31 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8302 (mtmm) REVERT: H 39 TYR cc_start: 0.8077 (t80) cc_final: 0.7833 (t80) REVERT: H 83 ARG cc_start: 0.8926 (mmt-90) cc_final: 0.8462 (mmt90) REVERT: H 90 GLU cc_start: 0.8988 (mm-30) cc_final: 0.7973 (mp0) REVERT: K 433 MET cc_start: 0.7366 (tmm) cc_final: 0.7102 (tmm) REVERT: K 470 MET cc_start: 0.9482 (tpp) cc_final: 0.9252 (tpp) REVERT: K 524 PHE cc_start: 0.8206 (m-80) cc_final: 0.7508 (t80) REVERT: K 570 LYS cc_start: 0.9272 (mppt) cc_final: 0.8856 (pptt) REVERT: K 674 MET cc_start: 0.7907 (tpt) cc_final: 0.7590 (tpt) outliers start: 15 outliers final: 3 residues processed: 169 average time/residue: 1.8308 time to fit residues: 334.8424 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 579 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 76 GLN G 73 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.065066 restraints weight = 46964.953| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.21 r_work: 0.3045 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17932 Z= 0.210 Angle : 0.615 7.336 25470 Z= 0.350 Chirality : 0.038 0.172 2883 Planarity : 0.004 0.040 2222 Dihedral : 29.188 179.589 4716 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.62 % Allowed : 13.01 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1357 helix: 1.60 (0.18), residues: 838 sheet: -2.44 (0.66), residues: 50 loop : -1.55 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 364 HIS 0.006 0.001 HIS D 46 PHE 0.015 0.001 PHE G 25 TYR 0.014 0.001 TYR K 499 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 932) hydrogen bonds : angle 3.43726 ( 2404) covalent geometry : bond 0.00471 (17932) covalent geometry : angle 0.61489 (25470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8637 (pm20) cc_final: 0.8437 (pm20) REVERT: C 92 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8519 (mm-30) REVERT: C 111 ILE cc_start: 0.8870 (pt) cc_final: 0.8586 (mt) REVERT: D 65 ASP cc_start: 0.8822 (t70) cc_final: 0.8334 (t0) REVERT: D 90 GLU cc_start: 0.8968 (mp0) cc_final: 0.8642 (mp0) REVERT: E 87 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8663 (t) REVERT: F 84 MET cc_start: 0.9400 (mmm) cc_final: 0.9157 (mmp) REVERT: F 93 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: F 95 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7510 (mtp85) REVERT: G 61 GLU cc_start: 0.8348 (tp30) cc_final: 0.8124 (tp30) REVERT: G 64 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8012 (tp30) REVERT: G 90 ASP cc_start: 0.8982 (t0) cc_final: 0.8736 (t0) REVERT: H 31 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8481 (mtmm) REVERT: H 39 TYR cc_start: 0.8086 (t80) cc_final: 0.7780 (t80) REVERT: H 83 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8490 (mmt90) REVERT: H 90 GLU cc_start: 0.8903 (mm-30) cc_final: 0.7878 (mp0) REVERT: H 102 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7837 (mm-30) REVERT: K 349 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7689 (tt) REVERT: K 433 MET cc_start: 0.7380 (tmm) cc_final: 0.7007 (tmt) REVERT: K 452 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7354 (m) REVERT: K 524 PHE cc_start: 0.8278 (m-80) cc_final: 0.7542 (t80) REVERT: K 570 LYS cc_start: 0.9252 (mppt) cc_final: 0.8969 (pmtt) REVERT: K 609 MET cc_start: 0.9099 (ptm) cc_final: 0.8643 (ppp) REVERT: K 674 MET cc_start: 0.7831 (tpt) cc_final: 0.7529 (tpt) outliers start: 19 outliers final: 4 residues processed: 158 average time/residue: 1.8848 time to fit residues: 321.2634 Evaluate side-chains 150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 452 VAL Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.098878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067347 restraints weight = 47273.414| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.21 r_work: 0.3089 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17932 Z= 0.163 Angle : 0.584 9.085 25470 Z= 0.333 Chirality : 0.036 0.176 2883 Planarity : 0.004 0.038 2222 Dihedral : 28.922 179.944 4716 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.87 % Allowed : 13.78 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1357 helix: 1.86 (0.18), residues: 834 sheet: -2.34 (0.64), residues: 55 loop : -1.32 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 364 HIS 0.003 0.001 HIS D 46 PHE 0.009 0.001 PHE K 381 TYR 0.012 0.001 TYR K 499 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 932) hydrogen bonds : angle 3.25187 ( 2404) covalent geometry : bond 0.00359 (17932) covalent geometry : angle 0.58402 (25470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8610 (pm20) cc_final: 0.8396 (pm20) REVERT: C 92 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8574 (mm-30) REVERT: D 65 ASP cc_start: 0.8811 (t70) cc_final: 0.8304 (t0) REVERT: D 90 GLU cc_start: 0.8945 (mp0) cc_final: 0.8474 (mp0) REVERT: E 59 GLU cc_start: 0.8936 (pm20) cc_final: 0.8730 (pm20) REVERT: E 87 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8588 (t) REVERT: F 93 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: F 95 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7612 (mtp85) REVERT: G 61 GLU cc_start: 0.8331 (tp30) cc_final: 0.8042 (tp30) REVERT: G 64 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8027 (tp30) REVERT: G 90 ASP cc_start: 0.9028 (t0) cc_final: 0.8693 (t0) REVERT: H 39 TYR cc_start: 0.8100 (t80) cc_final: 0.7778 (t80) REVERT: H 65 ASP cc_start: 0.8919 (t0) cc_final: 0.8657 (t0) REVERT: H 83 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8436 (mmt90) REVERT: H 90 GLU cc_start: 0.8947 (mm-30) cc_final: 0.7915 (mp0) REVERT: K 349 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7691 (tt) REVERT: K 433 MET cc_start: 0.7377 (tmm) cc_final: 0.7022 (tmt) REVERT: K 524 PHE cc_start: 0.8268 (m-80) cc_final: 0.7689 (t80) REVERT: K 570 LYS cc_start: 0.9225 (mppt) cc_final: 0.8945 (pmtt) REVERT: K 609 MET cc_start: 0.9069 (ptm) cc_final: 0.8595 (ppp) REVERT: K 674 MET cc_start: 0.7743 (tpt) cc_final: 0.7434 (tpt) outliers start: 22 outliers final: 7 residues processed: 171 average time/residue: 1.7288 time to fit residues: 320.5372 Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 35 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: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.098937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067177 restraints weight = 47554.245| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.25 r_work: 0.3100 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17932 Z= 0.159 Angle : 0.585 8.974 25470 Z= 0.332 Chirality : 0.036 0.212 2883 Planarity : 0.004 0.039 2222 Dihedral : 28.857 179.904 4716 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 14.97 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.07 (0.24), residues: 1357 helix: 1.97 (0.18), residues: 837 sheet: -2.15 (0.68), residues: 55 loop : -1.31 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 364 HIS 0.004 0.001 HIS D 46 PHE 0.017 0.001 PHE K 574 TYR 0.010 0.001 TYR K 499 ARG 0.009 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 932) hydrogen bonds : angle 3.20618 ( 2404) covalent geometry : bond 0.00351 (17932) covalent geometry : angle 0.58525 (25470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.798 Fit side-chains REVERT: A 59 GLU cc_start: 0.8591 (pm20) cc_final: 0.8335 (pm20) REVERT: C 92 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8526 (mm-30) REVERT: D 65 ASP cc_start: 0.8766 (t70) cc_final: 0.8289 (t0) REVERT: D 90 GLU cc_start: 0.8932 (mp0) cc_final: 0.8454 (mp0) REVERT: E 59 GLU cc_start: 0.8943 (pm20) cc_final: 0.8716 (pm20) REVERT: E 87 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8597 (t) REVERT: F 93 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: F 95 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7561 (mtp85) REVERT: G 61 GLU cc_start: 0.8350 (tp30) cc_final: 0.8032 (tp30) REVERT: G 64 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8038 (tp30) REVERT: G 90 ASP cc_start: 0.8976 (t0) cc_final: 0.8624 (t0) REVERT: H 31 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8476 (mtmm) REVERT: H 39 TYR cc_start: 0.8105 (t80) cc_final: 0.7767 (t80) REVERT: H 83 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8448 (mmt90) REVERT: H 90 GLU cc_start: 0.8953 (mm-30) cc_final: 0.7922 (mp0) REVERT: H 102 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7723 (mm-30) REVERT: K 349 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7795 (tt) REVERT: K 433 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6952 (tmt) REVERT: K 524 PHE cc_start: 0.8518 (m-80) cc_final: 0.7793 (t80) REVERT: K 570 LYS cc_start: 0.9245 (mppt) cc_final: 0.8981 (pmtt) REVERT: K 609 MET cc_start: 0.9077 (ptm) cc_final: 0.8539 (ppp) REVERT: K 674 MET cc_start: 0.7711 (tpt) cc_final: 0.7391 (tpt) outliers start: 24 outliers final: 8 residues processed: 165 average time/residue: 1.8168 time to fit residues: 324.3912 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 74 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.097850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065753 restraints weight = 47498.470| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.26 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17932 Z= 0.200 Angle : 0.609 11.414 25470 Z= 0.341 Chirality : 0.037 0.186 2883 Planarity : 0.004 0.041 2222 Dihedral : 28.950 179.163 4716 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.70 % Allowed : 15.99 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.12 (0.24), residues: 1357 helix: 2.03 (0.18), residues: 830 sheet: -2.05 (0.68), residues: 55 loop : -1.31 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 364 HIS 0.004 0.001 HIS D 46 PHE 0.016 0.001 PHE K 574 TYR 0.008 0.001 TYR G 57 ARG 0.009 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 932) hydrogen bonds : angle 3.25243 ( 2404) covalent geometry : bond 0.00450 (17932) covalent geometry : angle 0.60921 (25470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.424 Fit side-chains REVERT: A 59 GLU cc_start: 0.8591 (pm20) cc_final: 0.8354 (pm20) REVERT: C 92 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 65 ASP cc_start: 0.8788 (t70) cc_final: 0.8356 (t0) REVERT: D 90 GLU cc_start: 0.8998 (mp0) cc_final: 0.8506 (mp0) REVERT: E 87 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8676 (t) REVERT: F 93 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: F 95 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7529 (mtp85) REVERT: G 61 GLU cc_start: 0.8417 (tp30) cc_final: 0.8068 (tp30) REVERT: G 64 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8038 (tp30) REVERT: G 90 ASP cc_start: 0.8966 (t0) cc_final: 0.8613 (t0) REVERT: H 31 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8542 (mtmm) REVERT: H 39 TYR cc_start: 0.8147 (t80) cc_final: 0.7800 (t80) REVERT: H 83 ARG cc_start: 0.8939 (mmt-90) cc_final: 0.8493 (mmt90) REVERT: H 90 GLU cc_start: 0.8930 (mm-30) cc_final: 0.7882 (mp0) REVERT: K 349 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7818 (tt) REVERT: K 433 MET cc_start: 0.7386 (tmm) cc_final: 0.7023 (tmt) REVERT: K 524 PHE cc_start: 0.8515 (m-80) cc_final: 0.7853 (t80) REVERT: K 570 LYS cc_start: 0.9211 (mppt) cc_final: 0.8950 (pmtt) REVERT: K 609 MET cc_start: 0.9056 (ptm) cc_final: 0.8548 (ppp) REVERT: K 674 MET cc_start: 0.7664 (tpt) cc_final: 0.7379 (tpt) outliers start: 20 outliers final: 10 residues processed: 157 average time/residue: 1.8909 time to fit residues: 320.7269 Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 576 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 150 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** 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 = 0.3871 r_free = 0.3871 target = 0.098999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067200 restraints weight = 47144.555| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3096 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17932 Z= 0.153 Angle : 0.593 11.186 25470 Z= 0.332 Chirality : 0.036 0.183 2883 Planarity : 0.004 0.043 2222 Dihedral : 28.848 179.790 4716 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.87 % Allowed : 16.41 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.30 (0.24), residues: 1357 helix: 2.14 (0.18), residues: 831 sheet: -1.92 (0.69), residues: 55 loop : -1.18 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 384 HIS 0.005 0.001 HIS K 554 PHE 0.014 0.001 PHE K 574 TYR 0.010 0.001 TYR G 57 ARG 0.009 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 932) hydrogen bonds : angle 3.15519 ( 2404) covalent geometry : bond 0.00334 (17932) covalent geometry : angle 0.59303 (25470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.527 Fit side-chains REVERT: A 59 GLU cc_start: 0.8565 (pm20) cc_final: 0.8324 (pm20) REVERT: C 74 LYS cc_start: 0.9450 (mppt) cc_final: 0.9230 (mmtm) REVERT: C 92 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8525 (mm-30) REVERT: D 65 ASP cc_start: 0.8769 (t70) cc_final: 0.8321 (t0) REVERT: D 90 GLU cc_start: 0.8983 (mp0) cc_final: 0.8490 (mp0) REVERT: E 59 GLU cc_start: 0.8925 (pm20) cc_final: 0.8695 (pm20) REVERT: E 87 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8605 (t) REVERT: F 93 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: F 95 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: G 61 GLU cc_start: 0.8388 (tp30) cc_final: 0.8025 (tp30) REVERT: G 64 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8071 (tp30) REVERT: G 90 ASP cc_start: 0.8947 (t0) cc_final: 0.8553 (t0) REVERT: H 31 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8523 (mtmm) REVERT: H 39 TYR cc_start: 0.8118 (t80) cc_final: 0.7785 (t80) REVERT: H 65 ASP cc_start: 0.8904 (t0) cc_final: 0.8681 (t0) REVERT: H 83 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8467 (mmt90) REVERT: H 90 GLU cc_start: 0.8959 (mm-30) cc_final: 0.7935 (mp0) REVERT: K 349 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7821 (tt) REVERT: K 433 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6947 (tmt) REVERT: K 524 PHE cc_start: 0.8555 (m-80) cc_final: 0.7919 (t80) REVERT: K 570 LYS cc_start: 0.9198 (mppt) cc_final: 0.8949 (pmtt) REVERT: K 609 MET cc_start: 0.9048 (ptm) cc_final: 0.8535 (ppp) REVERT: K 674 MET cc_start: 0.7607 (tpt) cc_final: 0.7308 (tpt) outliers start: 22 outliers final: 8 residues processed: 159 average time/residue: 1.8487 time to fit residues: 318.1774 Evaluate side-chains 157 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.098561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066604 restraints weight = 47053.463| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.25 r_work: 0.3086 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17932 Z= 0.175 Angle : 0.601 12.063 25470 Z= 0.337 Chirality : 0.036 0.161 2883 Planarity : 0.004 0.045 2222 Dihedral : 28.816 179.427 4716 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.96 % Allowed : 16.92 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.22 (0.24), residues: 1357 helix: 2.08 (0.18), residues: 837 sheet: -1.82 (0.70), residues: 55 loop : -1.27 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 384 HIS 0.004 0.001 HIS K 554 PHE 0.015 0.001 PHE K 574 TYR 0.009 0.001 TYR G 57 ARG 0.009 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 932) hydrogen bonds : angle 3.20909 ( 2404) covalent geometry : bond 0.00391 (17932) covalent geometry : angle 0.60142 (25470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.660 Fit side-chains REVERT: A 59 GLU cc_start: 0.8546 (pm20) cc_final: 0.8290 (pm20) REVERT: C 92 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8558 (mm-30) REVERT: D 65 ASP cc_start: 0.8775 (t70) cc_final: 0.8313 (t0) REVERT: D 90 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: E 59 GLU cc_start: 0.8877 (pm20) cc_final: 0.8638 (pm20) REVERT: E 87 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8627 (t) REVERT: F 93 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: F 95 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: G 61 GLU cc_start: 0.8409 (tp30) cc_final: 0.8033 (tp30) REVERT: G 64 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8054 (tp30) REVERT: G 90 ASP cc_start: 0.8919 (t0) cc_final: 0.8515 (t0) REVERT: H 31 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8557 (mtmm) REVERT: H 65 ASP cc_start: 0.8924 (t0) cc_final: 0.8698 (t0) REVERT: H 83 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8467 (mmt90) REVERT: H 90 GLU cc_start: 0.8920 (mm-30) cc_final: 0.7876 (mp0) REVERT: H 102 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7677 (mm-30) REVERT: K 349 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7879 (tt) REVERT: K 433 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6924 (tmt) REVERT: K 524 PHE cc_start: 0.8570 (m-80) cc_final: 0.7969 (t80) REVERT: K 570 LYS cc_start: 0.9201 (mppt) cc_final: 0.8978 (pmtt) REVERT: K 609 MET cc_start: 0.9019 (ptm) cc_final: 0.8483 (ppp) REVERT: K 674 MET cc_start: 0.7619 (tpt) cc_final: 0.7312 (tpt) outliers start: 23 outliers final: 9 residues processed: 157 average time/residue: 1.8650 time to fit residues: 317.6985 Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 43 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** 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 = 0.3874 r_free = 0.3874 target = 0.099108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067281 restraints weight = 47478.828| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.27 r_work: 0.3104 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17932 Z= 0.152 Angle : 0.600 12.473 25470 Z= 0.335 Chirality : 0.036 0.167 2883 Planarity : 0.004 0.054 2222 Dihedral : 28.780 179.505 4716 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.79 % Allowed : 17.35 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.26 (0.24), residues: 1357 helix: 2.12 (0.18), residues: 837 sheet: -1.72 (0.70), residues: 55 loop : -1.28 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 384 HIS 0.004 0.001 HIS K 554 PHE 0.015 0.001 PHE K 574 TYR 0.011 0.001 TYR G 57 ARG 0.011 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 932) hydrogen bonds : angle 3.17687 ( 2404) covalent geometry : bond 0.00333 (17932) covalent geometry : angle 0.59971 (25470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.385 Fit side-chains REVERT: A 59 GLU cc_start: 0.8551 (pm20) cc_final: 0.8334 (pm20) REVERT: C 92 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8532 (mm-30) REVERT: D 65 ASP cc_start: 0.8766 (t70) cc_final: 0.8294 (t0) REVERT: D 90 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: E 59 GLU cc_start: 0.8905 (pm20) cc_final: 0.8632 (pm20) REVERT: E 87 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8579 (t) REVERT: F 84 MET cc_start: 0.9389 (mmm) cc_final: 0.9130 (mmp) REVERT: F 93 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: F 95 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7535 (mtp85) REVERT: G 61 GLU cc_start: 0.8394 (tp30) cc_final: 0.8017 (tp30) REVERT: G 64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8059 (tp30) REVERT: G 90 ASP cc_start: 0.8863 (t0) cc_final: 0.8470 (t0) REVERT: H 31 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8509 (mtmm) REVERT: H 39 TYR cc_start: 0.8092 (t80) cc_final: 0.7767 (t80) REVERT: H 65 ASP cc_start: 0.8889 (t0) cc_final: 0.8656 (t0) REVERT: H 83 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8453 (mmt90) REVERT: H 90 GLU cc_start: 0.8958 (mm-30) cc_final: 0.7900 (mp0) REVERT: K 349 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7876 (tt) REVERT: K 433 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6996 (tmt) REVERT: K 570 LYS cc_start: 0.9208 (mppt) cc_final: 0.8972 (pmtt) REVERT: K 674 MET cc_start: 0.7615 (tpt) cc_final: 0.7308 (tpt) outliers start: 21 outliers final: 9 residues processed: 153 average time/residue: 1.8586 time to fit residues: 306.9440 Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 138 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS ** K 565 ASN ** 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 = 0.3882 r_free = 0.3882 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067768 restraints weight = 47327.855| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3115 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17932 Z= 0.147 Angle : 0.605 12.891 25470 Z= 0.337 Chirality : 0.036 0.170 2883 Planarity : 0.004 0.045 2222 Dihedral : 28.734 179.603 4716 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.53 % Allowed : 17.60 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.30 (0.24), residues: 1357 helix: 2.14 (0.18), residues: 836 sheet: -1.61 (0.72), residues: 55 loop : -1.26 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP K 384 HIS 0.009 0.001 HIS H 106 PHE 0.010 0.001 PHE K 381 TYR 0.010 0.001 TYR G 57 ARG 0.011 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 932) hydrogen bonds : angle 3.16146 ( 2404) covalent geometry : bond 0.00324 (17932) covalent geometry : angle 0.60524 (25470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.420 Fit side-chains REVERT: A 59 GLU cc_start: 0.8552 (pm20) cc_final: 0.8332 (pm20) REVERT: C 92 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8538 (mm-30) REVERT: D 65 ASP cc_start: 0.8753 (t70) cc_final: 0.8289 (t0) REVERT: D 90 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: E 59 GLU cc_start: 0.8915 (pm20) cc_final: 0.8681 (pm20) REVERT: E 87 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8562 (t) REVERT: F 93 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8054 (mp10) REVERT: F 95 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7535 (mtp85) REVERT: G 61 GLU cc_start: 0.8382 (tp30) cc_final: 0.8004 (tp30) REVERT: G 64 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8042 (tp30) REVERT: G 90 ASP cc_start: 0.8875 (t0) cc_final: 0.8483 (t0) REVERT: H 31 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8516 (mtmm) REVERT: H 39 TYR cc_start: 0.8089 (t80) cc_final: 0.7762 (t80) REVERT: H 65 ASP cc_start: 0.8895 (t0) cc_final: 0.8656 (t0) REVERT: H 83 ARG cc_start: 0.8871 (mmt-90) cc_final: 0.8447 (mmt90) REVERT: H 90 GLU cc_start: 0.8963 (mm-30) cc_final: 0.7908 (mp0) REVERT: H 102 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7290 (mm-30) REVERT: K 349 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7908 (tt) REVERT: K 433 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6980 (tmt) REVERT: K 570 LYS cc_start: 0.9217 (mppt) cc_final: 0.8980 (pmtt) REVERT: K 609 MET cc_start: 0.8974 (ptm) cc_final: 0.8463 (ppp) REVERT: K 674 MET cc_start: 0.7539 (tpt) cc_final: 0.7225 (tpt) outliers start: 18 outliers final: 8 residues processed: 155 average time/residue: 1.8426 time to fit residues: 308.6611 Evaluate side-chains 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 344 THR Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 565 ASN ** 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 = 0.3881 r_free = 0.3881 target = 0.099487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067701 restraints weight = 47376.638| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.24 r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17932 Z= 0.158 Angle : 0.612 15.318 25470 Z= 0.337 Chirality : 0.036 0.168 2883 Planarity : 0.004 0.046 2222 Dihedral : 28.675 179.725 4716 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.70 % Allowed : 17.60 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.31 (0.24), residues: 1357 helix: 2.16 (0.18), residues: 834 sheet: -1.69 (0.70), residues: 59 loop : -1.25 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 384 HIS 0.004 0.001 HIS K 554 PHE 0.012 0.001 PHE K 574 TYR 0.010 0.001 TYR G 57 ARG 0.010 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 932) hydrogen bonds : angle 3.16982 ( 2404) covalent geometry : bond 0.00349 (17932) covalent geometry : angle 0.61175 (25470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11774.88 seconds wall clock time: 202 minutes 50.52 seconds (12170.52 seconds total)