Starting phenix.real_space_refine on Sat May 17 18:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnt_61626/05_2025/9jnt_61626.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9366 2.51 5 N 2985 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 16283 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4240 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 496} Chain breaks: 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: 8.64, per 1000 atoms: 0.53 Number of scatterers: 16283 At special positions: 0 Unit cell: (93.095, 116.91, 158.045, 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 25 16.00 P 294 15.00 Mg 1 11.99 O 3612 8.00 N 2985 7.00 C 9366 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: 3.85 Conformation dependent library (CDL) restraints added in 1.7 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 3.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 6.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.643A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.843A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.599A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.465A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (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 63 through 75 removed outlier: 3.539A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.606A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.032A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.557A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.512A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.133A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.857A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.519A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 115 No H-bonds generated for 'chain 'K' and resid 114 through 115' Processing helix chain 'K' and resid 116 through 119 removed outlier: 3.560A pdb=" N PHE K 119 " --> pdb=" O SER K 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 120 through 129 removed outlier: 4.279A pdb=" N ALA K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.089A pdb=" N GLN K 135 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 136 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 227 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 268 removed outlier: 4.228A pdb=" N GLU K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 removed outlier: 3.684A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.583A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 377 through 385 Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 476 removed outlier: 3.764A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 482 Processing helix chain 'K' and resid 494 through 498 removed outlier: 3.583A pdb=" N LEU K 497 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.550A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.840A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.065A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.770A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.803A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A 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: 7.001A 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 101 through 102 removed outlier: 6.958A 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: 6.814A 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: 6.976A 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 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 301 through 302 removed outlier: 7.579A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 427 through 431 556 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2188 1.32 - 1.44: 5908 1.44 - 1.57: 8450 1.57 - 1.69: 586 1.69 - 1.81: 43 Bond restraints: 17175 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.57e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.29e-02 6.01e+03 9.38e+00 bond pdb=" C PRO K 423 " pdb=" O PRO K 423 " ideal model delta sigma weight residual 1.232 1.200 0.033 1.20e-02 6.94e+03 7.44e+00 bond pdb=" CA PRO K 423 " pdb=" CB PRO K 423 " ideal model delta sigma weight residual 1.533 1.496 0.036 1.35e-02 5.49e+03 7.26e+00 bond pdb=" N THR K 419 " pdb=" CA THR K 419 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.28e+00 ... (remaining 17170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 23494 1.54 - 3.07: 827 3.07 - 4.61: 108 4.61 - 6.14: 26 6.14 - 7.68: 7 Bond angle restraints: 24462 Sorted by residual: angle pdb=" C LEU K 422 " pdb=" N PRO K 423 " pdb=" CA PRO K 423 " ideal model delta sigma weight residual 120.31 116.64 3.67 9.80e-01 1.04e+00 1.40e+01 angle pdb=" CA PRO K 423 " pdb=" C PRO K 423 " pdb=" N LYS K 424 " ideal model delta sigma weight residual 114.65 119.27 -4.62 1.27e+00 6.20e-01 1.32e+01 angle pdb=" CA PRO K 189 " pdb=" N PRO K 189 " pdb=" CD PRO K 189 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 angle pdb=" O VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 122.71 119.44 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N VAL B 21 " pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 112.96 109.73 3.23 1.00e+00 1.00e+00 1.04e+01 ... (remaining 24457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 8160 35.90 - 71.81: 1409 71.81 - 107.71: 19 107.71 - 143.61: 3 143.61 - 179.52: 11 Dihedral angle restraints: 9602 sinusoidal: 5855 harmonic: 3747 Sorted by residual: dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual -180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA HIS B 18 " pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 9599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2279 0.050 - 0.100: 422 0.100 - 0.150: 71 0.150 - 0.200: 5 0.200 - 0.251: 1 Chirality restraints: 2778 Sorted by residual: chirality pdb=" CA LEU K 421 " pdb=" N LEU K 421 " pdb=" C LEU K 421 " pdb=" CB LEU K 421 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" P DG I 99 " pdb=" OP1 DG I 99 " pdb=" OP2 DG I 99 " pdb=" O5' DG I 99 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CG LEU C 63 " pdb=" CB LEU C 63 " pdb=" CD1 LEU C 63 " pdb=" CD2 LEU C 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2775 not shown) Planarity restraints: 2087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO K 189 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 417 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C VAL K 417 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL K 417 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU K 418 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO K 489 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.029 5.00e-02 4.00e+02 ... (remaining 2084 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 118 2.57 - 3.15: 12519 3.15 - 3.73: 28110 3.73 - 4.32: 39262 4.32 - 4.90: 58382 Nonbonded interactions: 138391 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.985 2.170 nonbonded pdb=" O PRO K 372 " pdb=" OG SER K 376 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.165 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 2.190 3.040 nonbonded pdb=" O VAL K 398 " pdb=" ND1 HIS K 402 " model vdw 2.200 3.120 ... (remaining 138386 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' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 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: 0.900 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.110 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.005 0.087 17175 Z= 0.230 Angle : 0.667 7.680 24462 Z= 0.389 Chirality : 0.040 0.251 2778 Planarity : 0.005 0.111 2087 Dihedral : 26.481 179.516 7174 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.16 (0.25), residues: 1259 helix: 1.27 (0.19), residues: 768 sheet: -2.43 (0.66), residues: 62 loop : -1.63 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 364 HIS 0.006 0.001 HIS D 46 PHE 0.033 0.002 PHE K 381 TYR 0.016 0.001 TYR K 320 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.08890 ( 926) hydrogen bonds : angle 4.10263 ( 2378) covalent geometry : bond 0.00502 (17175) covalent geometry : angle 0.66653 (24462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8625 (pm20) REVERT: C 104 GLN cc_start: 0.8354 (mm110) cc_final: 0.7799 (mm110) REVERT: D 43 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8911 (mmtt) REVERT: D 90 GLU cc_start: 0.8759 (mp0) cc_final: 0.8406 (mp0) REVERT: E 59 GLU cc_start: 0.8313 (pm20) cc_final: 0.8103 (pm20) REVERT: E 77 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7948 (m-30) REVERT: G 75 LYS cc_start: 0.8801 (mttm) cc_final: 0.8487 (mmmt) REVERT: H 65 ASP cc_start: 0.8628 (t70) cc_final: 0.8052 (t0) REVERT: K 184 GLN cc_start: 0.8499 (pm20) cc_final: 0.8281 (mp10) REVERT: K 294 CYS cc_start: 0.8331 (m) cc_final: 0.7606 (t) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 1.7502 time to fit residues: 392.5763 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN E 68 GLN F 93 GLN G 73 ASN G 104 GLN K 86 ASN K 111 HIS K 317 ASN K 361 HIS K 617 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058130 restraints weight = 37505.048| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.32 r_work: 0.2768 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17175 Z= 0.281 Angle : 0.676 8.340 24462 Z= 0.373 Chirality : 0.041 0.164 2778 Planarity : 0.005 0.062 2087 Dihedral : 30.435 177.428 4613 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.37 % Allowed : 11.14 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.31 (0.25), residues: 1259 helix: 1.41 (0.19), residues: 775 sheet: -2.21 (0.65), residues: 69 loop : -1.70 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.014 0.001 PHE K 381 TYR 0.013 0.002 TYR H 34 ARG 0.009 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 926) hydrogen bonds : angle 3.52900 ( 2378) covalent geometry : bond 0.00652 (17175) covalent geometry : angle 0.67588 (24462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7580 (p-80) REVERT: A 59 GLU cc_start: 0.8870 (pm20) cc_final: 0.8433 (pm20) REVERT: B 24 ASP cc_start: 0.8366 (t0) cc_final: 0.8159 (t0) REVERT: C 90 ASP cc_start: 0.8398 (t0) cc_final: 0.8128 (t0) REVERT: D 90 GLU cc_start: 0.8860 (mp0) cc_final: 0.8602 (mp0) REVERT: E 59 GLU cc_start: 0.8405 (pm20) cc_final: 0.7885 (pm20) REVERT: E 77 ASP cc_start: 0.9022 (m-30) cc_final: 0.8745 (m-30) REVERT: E 106 ASP cc_start: 0.8460 (m-30) cc_final: 0.8209 (m-30) REVERT: E 123 ASP cc_start: 0.9118 (m-30) cc_final: 0.8888 (m-30) REVERT: G 64 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: H 65 ASP cc_start: 0.8752 (t70) cc_final: 0.8215 (t0) REVERT: K 294 CYS cc_start: 0.8134 (m) cc_final: 0.7319 (t) REVERT: K 568 ASP cc_start: 0.8435 (p0) cc_final: 0.8220 (p0) REVERT: K 655 ARG cc_start: 0.8333 (pmt-80) cc_final: 0.8096 (pmt-80) outliers start: 26 outliers final: 14 residues processed: 181 average time/residue: 1.6667 time to fit residues: 326.1987 Evaluate side-chains 173 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 126 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 93 GLN G 73 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063412 restraints weight = 37530.437| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.29 r_work: 0.2873 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17175 Z= 0.141 Angle : 0.598 6.717 24462 Z= 0.335 Chirality : 0.037 0.169 2778 Planarity : 0.004 0.054 2087 Dihedral : 29.873 175.528 4613 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.55 % Allowed : 14.89 % Favored : 83.56 % 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: 0.67 (0.25), residues: 1259 helix: 1.72 (0.19), residues: 777 sheet: -1.97 (0.68), residues: 67 loop : -1.64 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.007 0.001 HIS K 613 PHE 0.011 0.001 PHE K 574 TYR 0.011 0.001 TYR K 545 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 926) hydrogen bonds : angle 3.12655 ( 2378) covalent geometry : bond 0.00307 (17175) covalent geometry : angle 0.59794 (24462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8806 (pm20) cc_final: 0.8366 (pm20) REVERT: B 16 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7743 (mtpp) REVERT: E 59 GLU cc_start: 0.8483 (pm20) cc_final: 0.8104 (pm20) REVERT: E 77 ASP cc_start: 0.8977 (m-30) cc_final: 0.8681 (m-30) REVERT: E 120 MET cc_start: 0.7967 (mtt) cc_final: 0.7743 (mtt) REVERT: E 123 ASP cc_start: 0.9090 (m-30) cc_final: 0.8890 (m-30) REVERT: G 73 ASN cc_start: 0.8152 (m-40) cc_final: 0.7689 (t0) REVERT: H 65 ASP cc_start: 0.8656 (t70) cc_final: 0.8120 (t0) REVERT: K 196 LEU cc_start: 0.8934 (tt) cc_final: 0.8708 (tt) REVERT: K 263 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: K 568 ASP cc_start: 0.8266 (p0) cc_final: 0.7983 (p0) REVERT: K 586 ASN cc_start: 0.8985 (t0) cc_final: 0.8783 (t0) REVERT: K 655 ARG cc_start: 0.8337 (pmt-80) cc_final: 0.8089 (pmt-80) outliers start: 17 outliers final: 9 residues processed: 198 average time/residue: 1.5512 time to fit residues: 333.5171 Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 477 ASN K 505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.090985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061340 restraints weight = 37407.530| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.30 r_work: 0.2829 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17175 Z= 0.181 Angle : 0.609 7.173 24462 Z= 0.339 Chirality : 0.037 0.174 2778 Planarity : 0.004 0.054 2087 Dihedral : 29.907 176.728 4613 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 15.25 % Favored : 82.01 % 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: 0.73 (0.25), residues: 1259 helix: 1.75 (0.19), residues: 778 sheet: -1.98 (0.67), residues: 67 loop : -1.59 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.008 0.001 PHE K 381 TYR 0.010 0.001 TYR C 57 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 926) hydrogen bonds : angle 3.10293 ( 2378) covalent geometry : bond 0.00413 (17175) covalent geometry : angle 0.60881 (24462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8831 (pm20) cc_final: 0.8363 (pm20) REVERT: B 24 ASP cc_start: 0.8295 (t0) cc_final: 0.7929 (t0) REVERT: D 68 GLU cc_start: 0.8413 (pt0) cc_final: 0.8161 (tp30) REVERT: D 90 GLU cc_start: 0.8843 (mp0) cc_final: 0.8579 (mp0) REVERT: E 59 GLU cc_start: 0.8490 (pm20) cc_final: 0.8099 (pm20) REVERT: E 77 ASP cc_start: 0.8990 (m-30) cc_final: 0.8707 (m-30) REVERT: E 123 ASP cc_start: 0.9107 (m-30) cc_final: 0.8872 (m-30) REVERT: G 64 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: G 73 ASN cc_start: 0.8214 (m-40) cc_final: 0.7703 (t0) REVERT: H 65 ASP cc_start: 0.8695 (t70) cc_final: 0.8193 (t0) REVERT: K 196 LEU cc_start: 0.8919 (tt) cc_final: 0.8674 (tt) REVERT: K 263 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: K 568 ASP cc_start: 0.8311 (p0) cc_final: 0.8012 (p0) REVERT: K 586 ASN cc_start: 0.9067 (t0) cc_final: 0.8831 (t0) outliers start: 30 outliers final: 17 residues processed: 190 average time/residue: 1.6038 time to fit residues: 330.2677 Evaluate side-chains 184 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060896 restraints weight = 37639.758| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.34 r_work: 0.2818 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17175 Z= 0.192 Angle : 0.611 7.520 24462 Z= 0.341 Chirality : 0.037 0.160 2778 Planarity : 0.004 0.055 2087 Dihedral : 29.882 177.011 4613 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.20 % Allowed : 15.89 % Favored : 80.91 % 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: 0.76 (0.25), residues: 1259 helix: 1.82 (0.19), residues: 774 sheet: -2.16 (0.65), residues: 69 loop : -1.61 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.007 0.001 PHE A 67 TYR 0.010 0.001 TYR C 57 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 926) hydrogen bonds : angle 3.09385 ( 2378) covalent geometry : bond 0.00438 (17175) covalent geometry : angle 0.61138 (24462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8818 (pm20) cc_final: 0.8392 (pm20) REVERT: D 68 GLU cc_start: 0.8435 (pt0) cc_final: 0.8149 (tp30) REVERT: D 90 GLU cc_start: 0.8845 (mp0) cc_final: 0.8631 (mp0) REVERT: E 59 GLU cc_start: 0.8470 (pm20) cc_final: 0.7948 (pm20) REVERT: E 77 ASP cc_start: 0.8994 (m-30) cc_final: 0.8718 (m-30) REVERT: E 79 LYS cc_start: 0.9107 (tttm) cc_final: 0.8880 (tttp) REVERT: E 123 ASP cc_start: 0.9102 (m-30) cc_final: 0.8866 (m-30) REVERT: G 64 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: G 73 ASN cc_start: 0.8273 (m-40) cc_final: 0.7646 (t0) REVERT: G 75 LYS cc_start: 0.8568 (mttm) cc_final: 0.8312 (mmmt) REVERT: H 65 ASP cc_start: 0.8696 (t70) cc_final: 0.8194 (t0) REVERT: K 263 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8979 (mp0) REVERT: K 568 ASP cc_start: 0.8250 (p0) cc_final: 0.7973 (p0) REVERT: K 586 ASN cc_start: 0.9101 (t0) cc_final: 0.8863 (t0) outliers start: 35 outliers final: 21 residues processed: 185 average time/residue: 1.6347 time to fit residues: 328.4725 Evaluate side-chains 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061864 restraints weight = 37335.333| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.32 r_work: 0.2825 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17175 Z= 0.150 Angle : 0.607 7.617 24462 Z= 0.338 Chirality : 0.036 0.162 2778 Planarity : 0.004 0.054 2087 Dihedral : 29.838 176.891 4613 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.65 % Allowed : 17.35 % Favored : 80.00 % 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: 0.83 (0.25), residues: 1259 helix: 1.88 (0.19), residues: 773 sheet: -2.05 (0.66), residues: 67 loop : -1.60 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 PHE 0.007 0.001 PHE B 61 TYR 0.010 0.001 TYR C 57 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 926) hydrogen bonds : angle 3.03904 ( 2378) covalent geometry : bond 0.00333 (17175) covalent geometry : angle 0.60651 (24462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8829 (pm20) cc_final: 0.8440 (pm20) REVERT: B 24 ASP cc_start: 0.8096 (t0) cc_final: 0.7820 (t0) REVERT: D 68 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: D 90 GLU cc_start: 0.8830 (mp0) cc_final: 0.8584 (mp0) REVERT: E 59 GLU cc_start: 0.8469 (pm20) cc_final: 0.7970 (pm20) REVERT: E 77 ASP cc_start: 0.8992 (m-30) cc_final: 0.8716 (m-30) REVERT: E 123 ASP cc_start: 0.9114 (m-30) cc_final: 0.8904 (m-30) REVERT: G 64 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: G 73 ASN cc_start: 0.8210 (m-40) cc_final: 0.7623 (t0) REVERT: G 75 LYS cc_start: 0.8569 (mttm) cc_final: 0.8315 (mmmt) REVERT: H 65 ASP cc_start: 0.8687 (t70) cc_final: 0.8135 (t0) REVERT: K 196 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8392 (tm) REVERT: K 263 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8940 (mp0) REVERT: K 568 ASP cc_start: 0.8256 (p0) cc_final: 0.7967 (p0) REVERT: K 586 ASN cc_start: 0.9102 (t0) cc_final: 0.8841 (t0) REVERT: K 596 TYR cc_start: 0.9175 (t80) cc_final: 0.8945 (t80) outliers start: 29 outliers final: 20 residues processed: 185 average time/residue: 1.6913 time to fit residues: 339.5371 Evaluate side-chains 186 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 477 ASN Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.060729 restraints weight = 37232.621| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.31 r_work: 0.2804 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17175 Z= 0.200 Angle : 0.620 8.905 24462 Z= 0.344 Chirality : 0.038 0.160 2778 Planarity : 0.004 0.055 2087 Dihedral : 29.844 177.177 4613 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.01 % Allowed : 18.08 % Favored : 78.90 % 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: 0.79 (0.25), residues: 1259 helix: 1.86 (0.19), residues: 773 sheet: -2.22 (0.64), residues: 69 loop : -1.60 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 PHE 0.007 0.001 PHE A 67 TYR 0.010 0.001 TYR C 57 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 926) hydrogen bonds : angle 3.07929 ( 2378) covalent geometry : bond 0.00458 (17175) covalent geometry : angle 0.61972 (24462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8804 (pm20) cc_final: 0.8361 (pm20) REVERT: B 24 ASP cc_start: 0.8118 (t0) cc_final: 0.7827 (t0) REVERT: C 90 ASP cc_start: 0.8332 (t0) cc_final: 0.8040 (t0) REVERT: D 68 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: D 90 GLU cc_start: 0.8835 (mp0) cc_final: 0.8571 (mp0) REVERT: E 59 GLU cc_start: 0.8463 (pm20) cc_final: 0.7897 (pm20) REVERT: E 77 ASP cc_start: 0.8987 (m-30) cc_final: 0.8709 (m-30) REVERT: E 123 ASP cc_start: 0.9094 (m-30) cc_final: 0.8855 (m-30) REVERT: G 64 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: G 73 ASN cc_start: 0.8290 (m-40) cc_final: 0.7665 (t0) REVERT: G 75 LYS cc_start: 0.8584 (mttm) cc_final: 0.8332 (mmmt) REVERT: H 65 ASP cc_start: 0.8687 (t70) cc_final: 0.8186 (t0) REVERT: K 196 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8312 (tm) REVERT: K 385 PHE cc_start: 0.6345 (t80) cc_final: 0.5977 (t80) REVERT: K 568 ASP cc_start: 0.8291 (p0) cc_final: 0.8042 (p0) REVERT: K 586 ASN cc_start: 0.9135 (t0) cc_final: 0.8883 (t0) outliers start: 33 outliers final: 19 residues processed: 184 average time/residue: 1.6230 time to fit residues: 324.2739 Evaluate side-chains 186 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 476 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 104 GLN K 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060427 restraints weight = 37075.805| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.34 r_work: 0.2822 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17175 Z= 0.171 Angle : 0.623 8.600 24462 Z= 0.345 Chirality : 0.037 0.206 2778 Planarity : 0.004 0.055 2087 Dihedral : 29.841 177.135 4613 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.74 % Allowed : 18.90 % Favored : 78.36 % 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: 0.81 (0.25), residues: 1259 helix: 1.87 (0.19), residues: 773 sheet: -2.18 (0.65), residues: 69 loop : -1.59 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 PHE 0.007 0.001 PHE B 61 TYR 0.010 0.001 TYR A 54 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 926) hydrogen bonds : angle 3.08083 ( 2378) covalent geometry : bond 0.00389 (17175) covalent geometry : angle 0.62331 (24462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8805 (pm20) cc_final: 0.8363 (pm20) REVERT: B 24 ASP cc_start: 0.8129 (t0) cc_final: 0.7837 (t0) REVERT: C 90 ASP cc_start: 0.8337 (t0) cc_final: 0.8047 (t0) REVERT: D 65 ASP cc_start: 0.8867 (t0) cc_final: 0.8665 (t0) REVERT: D 68 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: D 90 GLU cc_start: 0.8843 (mp0) cc_final: 0.8566 (mp0) REVERT: E 59 GLU cc_start: 0.8454 (pm20) cc_final: 0.7902 (pm20) REVERT: E 77 ASP cc_start: 0.9005 (m-30) cc_final: 0.8734 (m-30) REVERT: E 123 ASP cc_start: 0.9115 (m-30) cc_final: 0.8895 (m-30) REVERT: G 64 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: G 73 ASN cc_start: 0.8291 (m-40) cc_final: 0.7663 (t0) REVERT: G 75 LYS cc_start: 0.8599 (mttm) cc_final: 0.8347 (mmmt) REVERT: H 65 ASP cc_start: 0.8700 (t70) cc_final: 0.8199 (t0) REVERT: K 196 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8317 (tm) REVERT: K 299 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8536 (p) REVERT: K 385 PHE cc_start: 0.6324 (t80) cc_final: 0.5958 (t80) REVERT: K 568 ASP cc_start: 0.8269 (p0) cc_final: 0.7987 (p0) REVERT: K 586 ASN cc_start: 0.9132 (t0) cc_final: 0.8878 (t0) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 1.6440 time to fit residues: 327.9433 Evaluate side-chains 191 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2076 > 50: distance: 38 - 44: 31.788 distance: 44 - 45: 37.169 distance: 45 - 46: 40.468 distance: 45 - 48: 55.623 distance: 46 - 47: 40.565 distance: 46 - 53: 39.142 distance: 48 - 49: 40.734 distance: 50 - 52: 39.661 distance: 53 - 54: 57.206 distance: 54 - 55: 40.654 distance: 54 - 57: 55.254 distance: 55 - 56: 56.088 distance: 55 - 58: 39.983 distance: 58 - 59: 11.909 distance: 59 - 60: 28.658 distance: 59 - 62: 50.130 distance: 60 - 68: 56.650 distance: 63 - 64: 39.656 distance: 64 - 66: 39.608 distance: 65 - 67: 56.701 distance: 68 - 69: 40.069 distance: 69 - 70: 38.750 distance: 69 - 72: 55.722 distance: 70 - 71: 52.628 distance: 70 - 79: 41.534 distance: 72 - 73: 40.837 distance: 73 - 74: 40.260 distance: 74 - 75: 39.359 distance: 75 - 76: 38.853 distance: 76 - 77: 39.717 distance: 79 - 80: 39.286 distance: 80 - 81: 39.121 distance: 81 - 82: 41.252 distance: 81 - 87: 6.381 distance: 83 - 84: 40.479 distance: 83 - 85: 40.731 distance: 84 - 86: 40.667 distance: 88 - 89: 30.435 distance: 89 - 90: 19.524 distance: 89 - 96: 7.968 distance: 91 - 92: 39.987 distance: 94 - 95: 40.378 distance: 97 - 98: 40.440 distance: 98 - 99: 40.050 distance: 98 - 104: 42.844 distance: 100 - 101: 56.229 distance: 101 - 103: 39.658 distance: 104 - 105: 43.894 distance: 105 - 106: 55.612 distance: 106 - 107: 41.114 distance: 106 - 113: 40.314 distance: 108 - 109: 39.489 distance: 109 - 110: 40.937 distance: 110 - 111: 10.208 distance: 113 - 114: 39.710 distance: 114 - 117: 69.824 distance: 115 - 116: 39.014 distance: 115 - 122: 40.792 distance: 117 - 118: 41.493 distance: 119 - 121: 44.268 distance: 122 - 123: 39.823 distance: 123 - 124: 53.176 distance: 124 - 125: 5.453 distance: 124 - 128: 30.834 distance: 125 - 147: 31.616 distance: 196 - 209: 3.325