Starting phenix.real_space_refine on Thu Sep 18 10:22:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnt_61626/09_2025/9jnt_61626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnt_61626/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jnt_61626/09_2025/9jnt_61626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnt_61626/09_2025/9jnt_61626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnt_61626/09_2025/9jnt_61626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnt_61626/09_2025/9jnt_61626.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.85, per 1000 atoms: 0.24 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: 1.56 Conformation dependent library (CDL) restraints added in 535.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.12 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: 4.04 Time building geometry restraints manager: 2.11 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG A 52 TYR 0.016 0.001 TYR K 320 PHE 0.033 0.002 PHE K 381 TRP 0.018 0.002 TRP K 364 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00502 (17175) covalent geometry : angle 0.66653 (24462) hydrogen bonds : bond 0.08890 ( 926) hydrogen bonds : angle 4.10263 ( 2378) *********************** 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 : 0.318 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: 0.9052 time to fit residues: 202.0184 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 : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 K 86 ASN K 111 HIS K 361 HIS K 617 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058446 restraints weight = 37639.809| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.34 r_work: 0.2760 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 17175 Z= 0.300 Angle : 0.685 8.539 24462 Z= 0.378 Chirality : 0.042 0.166 2778 Planarity : 0.005 0.062 2087 Dihedral : 30.471 177.607 4613 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.28 % Allowed : 11.05 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1259 helix: 1.39 (0.19), residues: 775 sheet: -2.22 (0.65), residues: 69 loop : -1.71 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.013 0.002 TYR H 34 PHE 0.015 0.001 PHE K 381 TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00693 (17175) covalent geometry : angle 0.68515 (24462) hydrogen bonds : bond 0.04865 ( 926) hydrogen bonds : angle 3.56089 ( 2378) *********************** 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 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7585 (p-80) REVERT: A 59 GLU cc_start: 0.8866 (pm20) cc_final: 0.8432 (pm20) REVERT: A 81 ASP cc_start: 0.8690 (t0) cc_final: 0.8488 (t0) REVERT: C 90 ASP cc_start: 0.8388 (t0) cc_final: 0.8091 (t0) REVERT: D 90 GLU cc_start: 0.8867 (mp0) cc_final: 0.8609 (mp0) REVERT: E 59 GLU cc_start: 0.8394 (pm20) cc_final: 0.7870 (pm20) REVERT: E 77 ASP cc_start: 0.9025 (m-30) cc_final: 0.8750 (m-30) REVERT: E 106 ASP cc_start: 0.8467 (m-30) cc_final: 0.8213 (m-30) REVERT: E 123 ASP cc_start: 0.9121 (m-30) cc_final: 0.8883 (m-30) REVERT: G 64 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: H 65 ASP cc_start: 0.8757 (t70) cc_final: 0.8212 (t0) REVERT: K 294 CYS cc_start: 0.8134 (m) cc_final: 0.7317 (t) REVERT: K 568 ASP cc_start: 0.8444 (p0) cc_final: 0.8154 (p0) REVERT: K 655 ARG cc_start: 0.8295 (pmt-80) cc_final: 0.8075 (pmt-80) outliers start: 25 outliers final: 12 residues processed: 178 average time/residue: 0.8717 time to fit residues: 167.2125 Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 82 LYS Chi-restraints excluded: chain E residue 87 SER 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 50 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN G 104 GLN K 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059954 restraints weight = 37694.379| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.32 r_work: 0.2803 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17175 Z= 0.153 Angle : 0.634 9.677 24462 Z= 0.352 Chirality : 0.038 0.167 2778 Planarity : 0.004 0.053 2087 Dihedral : 30.411 176.855 4613 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.01 % Allowed : 14.16 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1259 helix: 1.56 (0.19), residues: 775 sheet: -2.13 (0.67), residues: 69 loop : -1.63 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.011 0.001 TYR H 34 PHE 0.011 0.001 PHE K 381 TRP 0.017 0.001 TRP K 364 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00338 (17175) covalent geometry : angle 0.63372 (24462) hydrogen bonds : bond 0.04140 ( 926) hydrogen bonds : angle 3.34606 ( 2378) *********************** 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 195 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7490 (p-80) REVERT: A 59 GLU cc_start: 0.8846 (pm20) cc_final: 0.8368 (pm20) REVERT: A 81 ASP cc_start: 0.8699 (t0) cc_final: 0.8397 (t0) REVERT: B 16 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7771 (mtpp) REVERT: E 59 GLU cc_start: 0.8454 (pm20) cc_final: 0.7927 (pm20) REVERT: E 77 ASP cc_start: 0.9027 (m-30) cc_final: 0.8747 (m-30) REVERT: E 105 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: E 123 ASP cc_start: 0.9118 (m-30) cc_final: 0.8885 (m-30) REVERT: F 85 ASP cc_start: 0.8845 (m-30) cc_final: 0.8594 (m-30) REVERT: G 64 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: H 65 ASP cc_start: 0.8728 (t70) cc_final: 0.8205 (t0) REVERT: K 294 CYS cc_start: 0.8040 (m) cc_final: 0.7208 (t) REVERT: K 568 ASP cc_start: 0.8324 (p0) cc_final: 0.8041 (p0) REVERT: K 655 ARG cc_start: 0.8407 (pmt-80) cc_final: 0.8171 (pmt-80) outliers start: 22 outliers final: 11 residues processed: 182 average time/residue: 0.8866 time to fit residues: 174.0219 Evaluate side-chains 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 34 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 F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET 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 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN H 81 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 = 0.3620 r_free = 0.3620 target = 0.092555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063233 restraints weight = 37907.433| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.29 r_work: 0.2873 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17175 Z= 0.148 Angle : 0.597 8.080 24462 Z= 0.334 Chirality : 0.036 0.165 2778 Planarity : 0.004 0.055 2087 Dihedral : 29.815 175.486 4613 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.25), residues: 1259 helix: 1.76 (0.19), residues: 778 sheet: -2.06 (0.67), residues: 67 loop : -1.59 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE K 574 TRP 0.016 0.001 TRP K 364 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00326 (17175) covalent geometry : angle 0.59690 (24462) hydrogen bonds : bond 0.03522 ( 926) hydrogen bonds : angle 3.07395 ( 2378) *********************** 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: 24 poor density : 179 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8839 (pm20) cc_final: 0.8460 (pm20) REVERT: B 16 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7710 (mtpp) REVERT: D 68 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8074 (tp30) REVERT: D 90 GLU cc_start: 0.8862 (mp0) cc_final: 0.8592 (mp0) REVERT: E 59 GLU cc_start: 0.8496 (pm20) cc_final: 0.8125 (pm20) REVERT: E 77 ASP cc_start: 0.8984 (m-30) cc_final: 0.8692 (m-30) REVERT: G 64 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: G 73 ASN cc_start: 0.8150 (m-40) cc_final: 0.7743 (t0) REVERT: H 65 ASP cc_start: 0.8641 (t70) cc_final: 0.8074 (t0) REVERT: K 91 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8353 (tp) REVERT: K 263 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8819 (mp0) REVERT: K 568 ASP cc_start: 0.8308 (p0) cc_final: 0.8036 (p0) REVERT: K 655 ARG cc_start: 0.8337 (pmt-80) cc_final: 0.8081 (pmt-80) outliers start: 24 outliers final: 15 residues processed: 192 average time/residue: 0.7938 time to fit residues: 164.7513 Evaluate side-chains 182 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 91 LEU 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 409 LEU 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 72 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 142 optimal weight: 0.0170 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057801 restraints weight = 37505.402| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.35 r_work: 0.2736 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 17175 Z= 0.382 Angle : 0.710 9.082 24462 Z= 0.390 Chirality : 0.045 0.175 2778 Planarity : 0.005 0.056 2087 Dihedral : 30.453 178.801 4613 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.47 % Allowed : 16.35 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1259 helix: 1.48 (0.19), residues: 780 sheet: -2.29 (0.64), residues: 69 loop : -1.65 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 95 TYR 0.015 0.002 TYR H 34 PHE 0.011 0.002 PHE A 78 TRP 0.011 0.001 TRP K 364 HIS 0.007 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00884 (17175) covalent geometry : angle 0.70975 (24462) hydrogen bonds : bond 0.05314 ( 926) hydrogen bonds : angle 3.41388 ( 2378) *********************** 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 197 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7435 (p-80) REVERT: A 59 GLU cc_start: 0.8877 (pm20) cc_final: 0.8370 (pm20) REVERT: C 90 ASP cc_start: 0.8320 (t0) cc_final: 0.7935 (t0) REVERT: D 68 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: D 90 GLU cc_start: 0.8863 (mp0) cc_final: 0.8612 (mp0) REVERT: E 59 GLU cc_start: 0.8386 (pm20) cc_final: 0.7813 (pm20) REVERT: E 77 ASP cc_start: 0.9029 (m-30) cc_final: 0.8758 (m-30) REVERT: G 64 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: G 73 ASN cc_start: 0.8552 (m-40) cc_final: 0.7751 (t0) REVERT: H 65 ASP cc_start: 0.8800 (t70) cc_final: 0.8259 (t0) REVERT: K 109 PHE cc_start: 0.8147 (m-80) cc_final: 0.7902 (m-80) REVERT: K 256 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9173 (p) REVERT: K 568 ASP cc_start: 0.8292 (p0) cc_final: 0.8043 (p0) outliers start: 38 outliers final: 20 residues processed: 180 average time/residue: 0.7702 time to fit residues: 150.1739 Evaluate side-chains 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 56 LYS 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 74 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 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 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 256 THR 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 9 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060037 restraints weight = 37392.998| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.29 r_work: 0.2776 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17175 Z= 0.159 Angle : 0.646 8.261 24462 Z= 0.358 Chirality : 0.039 0.257 2778 Planarity : 0.004 0.056 2087 Dihedral : 30.413 177.507 4613 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.83 % Allowed : 17.99 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1259 helix: 1.62 (0.19), residues: 772 sheet: -2.12 (0.66), residues: 69 loop : -1.58 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.010 0.001 TYR H 34 PHE 0.009 0.001 PHE K 574 TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS K 211 Details of bonding type rmsd covalent geometry : bond 0.00356 (17175) covalent geometry : angle 0.64571 (24462) hydrogen bonds : bond 0.04293 ( 926) hydrogen bonds : angle 3.23462 ( 2378) *********************** 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 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8829 (pm20) cc_final: 0.8336 (pm20) REVERT: B 16 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7747 (mtpp) REVERT: C 90 ASP cc_start: 0.8263 (t0) cc_final: 0.7871 (t0) REVERT: D 68 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: D 90 GLU cc_start: 0.8819 (mp0) cc_final: 0.8577 (mp0) REVERT: E 59 GLU cc_start: 0.8430 (pm20) cc_final: 0.7830 (pm20) REVERT: E 77 ASP cc_start: 0.9041 (m-30) cc_final: 0.8764 (m-30) REVERT: G 64 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: G 73 ASN cc_start: 0.8469 (m-40) cc_final: 0.7665 (t0) REVERT: G 75 LYS cc_start: 0.8559 (mttm) cc_final: 0.8306 (mmmt) REVERT: H 65 ASP cc_start: 0.8769 (t70) cc_final: 0.8149 (t0) REVERT: K 256 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9144 (p) REVERT: K 299 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8458 (p) REVERT: K 385 PHE cc_start: 0.6656 (t80) cc_final: 0.6181 (t80) REVERT: K 568 ASP cc_start: 0.8265 (p0) cc_final: 0.8003 (p0) outliers start: 31 outliers final: 15 residues processed: 182 average time/residue: 0.8397 time to fit residues: 165.0448 Evaluate side-chains 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 LYS Chi-restraints excluded: chain C residue 78 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 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 K residue 256 THR Chi-restraints excluded: chain K residue 299 VAL 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 504 LEU 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 51 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.059330 restraints weight = 37338.783| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.31 r_work: 0.2776 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17175 Z= 0.239 Angle : 0.650 8.889 24462 Z= 0.359 Chirality : 0.039 0.246 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.157 176.951 4613 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.20 % Allowed : 19.18 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1259 helix: 1.66 (0.19), residues: 773 sheet: -2.16 (0.65), residues: 69 loop : -1.67 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.015 0.001 TYR K 320 PHE 0.008 0.001 PHE A 67 TRP 0.013 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00551 (17175) covalent geometry : angle 0.64965 (24462) hydrogen bonds : bond 0.04336 ( 926) hydrogen bonds : angle 3.21250 ( 2378) *********************** 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 194 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8847 (pm20) cc_final: 0.8393 (pm20) REVERT: B 16 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7771 (mtpp) REVERT: C 90 ASP cc_start: 0.8311 (t0) cc_final: 0.7929 (t0) REVERT: D 68 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: D 90 GLU cc_start: 0.8882 (mp0) cc_final: 0.8587 (mp0) REVERT: E 59 GLU cc_start: 0.8494 (pm20) cc_final: 0.7889 (pm20) REVERT: E 77 ASP cc_start: 0.9026 (m-30) cc_final: 0.8754 (m-30) REVERT: G 64 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: G 73 ASN cc_start: 0.8418 (m-40) cc_final: 0.7739 (t0) REVERT: H 65 ASP cc_start: 0.8740 (t70) cc_final: 0.8182 (t0) REVERT: K 385 PHE cc_start: 0.6518 (t80) cc_final: 0.6042 (t80) REVERT: K 568 ASP cc_start: 0.8292 (p0) cc_final: 0.8005 (p0) outliers start: 35 outliers final: 20 residues processed: 176 average time/residue: 0.8726 time to fit residues: 165.6176 Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 THR Chi-restraints excluded: chain C residue 113 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 53 SER Chi-restraints excluded: chain H residue 120 SER 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 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060248 restraints weight = 37179.311| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.29 r_work: 0.2782 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17175 Z= 0.167 Angle : 0.637 8.701 24462 Z= 0.352 Chirality : 0.038 0.269 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.155 176.785 4613 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.65 % Allowed : 19.82 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1259 helix: 1.72 (0.19), residues: 773 sheet: -2.13 (0.66), residues: 69 loop : -1.65 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.013 0.001 TYR K 320 PHE 0.008 0.001 PHE B 61 TRP 0.014 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00380 (17175) covalent geometry : angle 0.63665 (24462) hydrogen bonds : bond 0.04119 ( 926) hydrogen bonds : angle 3.17077 ( 2378) *********************** 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 190 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8834 (pm20) cc_final: 0.8377 (pm20) REVERT: B 16 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7746 (mtpp) REVERT: C 90 ASP cc_start: 0.8263 (t0) cc_final: 0.7902 (t0) REVERT: D 68 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: D 90 GLU cc_start: 0.8870 (mp0) cc_final: 0.8577 (mp0) REVERT: E 59 GLU cc_start: 0.8472 (pm20) cc_final: 0.7861 (pm20) REVERT: E 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8748 (m-30) REVERT: G 64 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: G 73 ASN cc_start: 0.8361 (m-40) cc_final: 0.7614 (t0) REVERT: G 75 LYS cc_start: 0.8579 (mttm) cc_final: 0.8336 (mmmt) REVERT: H 65 ASP cc_start: 0.8726 (t70) cc_final: 0.8219 (t0) REVERT: K 299 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8507 (p) REVERT: K 385 PHE cc_start: 0.6559 (t80) cc_final: 0.6082 (t80) REVERT: K 568 ASP cc_start: 0.8275 (p0) cc_final: 0.7993 (p0) outliers start: 29 outliers final: 22 residues processed: 174 average time/residue: 0.8766 time to fit residues: 164.4922 Evaluate side-chains 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 78 ILE Chi-restraints excluded: chain C residue 101 THR 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 104 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 299 VAL 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 504 LEU 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 ************** Weight determination summary: number of chunks: 151 random chunks: chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060532 restraints weight = 37129.631| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.28 r_work: 0.2791 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1535 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= 0.177 Angle : 0.637 9.753 24462 Z= 0.352 Chirality : 0.038 0.274 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.089 176.837 4613 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.47 % Allowed : 19.91 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.25), residues: 1259 helix: 1.76 (0.19), residues: 773 sheet: -2.14 (0.66), residues: 69 loop : -1.66 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.013 0.001 TYR K 320 PHE 0.008 0.001 PHE B 61 TRP 0.014 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00403 (17175) covalent geometry : angle 0.63711 (24462) hydrogen bonds : bond 0.03957 ( 926) hydrogen bonds : angle 3.13796 ( 2378) *********************** REFINEMENT MACRO_CYCLE 9 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 184 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8839 (pm20) cc_final: 0.8381 (pm20) REVERT: B 16 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7743 (mtpp) REVERT: C 90 ASP cc_start: 0.8314 (t0) cc_final: 0.7938 (t0) REVERT: D 68 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: D 90 GLU cc_start: 0.8878 (mp0) cc_final: 0.8579 (mp0) REVERT: E 59 GLU cc_start: 0.8498 (pm20) cc_final: 0.7866 (pm20) REVERT: E 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8748 (m-30) REVERT: G 64 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: G 73 ASN cc_start: 0.8341 (m-40) cc_final: 0.7623 (t0) REVERT: G 75 LYS cc_start: 0.8594 (mttm) cc_final: 0.8353 (mmmt) REVERT: H 65 ASP cc_start: 0.8727 (t70) cc_final: 0.8155 (t0) REVERT: K 299 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (p) REVERT: K 385 PHE cc_start: 0.6520 (t80) cc_final: 0.6076 (t80) REVERT: K 568 ASP cc_start: 0.8251 (p0) cc_final: 0.7980 (p0) outliers start: 27 outliers final: 20 residues processed: 169 average time/residue: 0.8594 time to fit residues: 156.2776 Evaluate side-chains 179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 78 ILE Chi-restraints excluded: chain C residue 101 THR 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 F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 299 VAL 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 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 113 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.089221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059095 restraints weight = 37370.077| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.33 r_work: 0.2770 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17175 Z= 0.254 Angle : 0.661 9.874 24462 Z= 0.364 Chirality : 0.040 0.275 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.133 177.042 4613 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.47 % Allowed : 20.00 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.24), residues: 1259 helix: 1.69 (0.19), residues: 773 sheet: -2.17 (0.65), residues: 69 loop : -1.68 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.013 0.001 TYR A 54 PHE 0.010 0.001 PHE K 385 TRP 0.012 0.001 TRP K 364 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00589 (17175) covalent geometry : angle 0.66134 (24462) hydrogen bonds : bond 0.04480 ( 926) hydrogen bonds : angle 3.20674 ( 2378) ********************** REFINEMENT MACRO_CYCLE 10 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 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8862 (pm20) cc_final: 0.8401 (pm20) REVERT: B 16 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7734 (mtpp) REVERT: C 90 ASP cc_start: 0.8345 (t0) cc_final: 0.7992 (t0) REVERT: D 68 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: D 90 GLU cc_start: 0.8888 (mp0) cc_final: 0.8675 (mp0) REVERT: E 59 GLU cc_start: 0.8427 (pm20) cc_final: 0.7836 (pm20) REVERT: E 77 ASP cc_start: 0.9000 (m-30) cc_final: 0.8716 (m-30) REVERT: G 64 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: G 73 ASN cc_start: 0.8406 (m-40) cc_final: 0.7728 (t0) REVERT: H 65 ASP cc_start: 0.8745 (t70) cc_final: 0.8192 (t0) REVERT: K 225 LEU cc_start: 0.9580 (tp) cc_final: 0.9303 (tt) REVERT: K 299 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (p) REVERT: K 385 PHE cc_start: 0.6519 (t80) cc_final: 0.6122 (t80) REVERT: K 568 ASP cc_start: 0.8266 (p0) cc_final: 0.8041 (p0) outliers start: 27 outliers final: 20 residues processed: 170 average time/residue: 0.8101 time to fit residues: 148.1324 Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP 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 101 THR 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 H residue 53 SER Chi-restraints excluded: chain K residue 299 VAL 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 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.090400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060446 restraints weight = 37399.004| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.31 r_work: 0.2786 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17175 Z= 0.170 Angle : 0.639 9.368 24462 Z= 0.353 Chirality : 0.038 0.262 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.069 176.966 4613 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.65 % Allowed : 19.82 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1259 helix: 1.78 (0.19), residues: 773 sheet: -2.14 (0.66), residues: 69 loop : -1.66 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.014 0.001 TYR K 320 PHE 0.021 0.001 PHE A 78 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00388 (17175) covalent geometry : angle 0.63946 (24462) hydrogen bonds : bond 0.03948 ( 926) hydrogen bonds : angle 3.12462 ( 2378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6106.50 seconds wall clock time: 104 minutes 31.82 seconds (6271.82 seconds total)