Starting phenix.real_space_refine on Wed Sep 17 03:46:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.map" model { file = "/net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lc9_23270/09_2025/7lc9_23270.cif" } resolution = 3.2 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= 0.001 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: 3 Type Number sf(0) Gaussians C 2170 2.51 5 N 611 2.21 5 O 716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 3497 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 254 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "A" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 254 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 254 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 254 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 254 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 181 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 341 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.26, per 1000 atoms: 0.36 Number of scatterers: 3497 At special positions: 0 Unit cell: (73.87, 78.85, 45.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 716 8.00 N 611 7.00 C 2170 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: 0.31 Conformation dependent library (CDL) restraints added in 152.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 60.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.904A pdb=" N VAL F 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N VAL H 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL J 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN I 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 70 through 85 removed outlier: 6.396A pdb=" N VAL F 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL H 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY F 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA H 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LYS H 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN F 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL H 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR F 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY H 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLU F 83 " --> pdb=" O GLY H 84 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL H 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL I 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY H 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA I 76 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR H 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LYS I 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN H 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL I 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR H 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY I 84 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU H 83 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL I 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL J 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY I 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA J 76 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LYS J 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN I 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL J 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR I 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY J 84 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLU I 83 " --> pdb=" O GLY J 84 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL J 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR K 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY K 84 " --> pdb=" O GLU J 83 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA J 85 " --> pdb=" O GLY K 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL K 71 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR L 72 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY K 73 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY L 84 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA K 85 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 88 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 65 removed outlier: 6.902A pdb=" N LYS B 60 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU A 61 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 63 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 64 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN A 65 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS C 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYS C 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR B 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N GLN C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N GLU D 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA C 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N THR D 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS C 58 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N GLU D 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL D 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA E 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL D 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS E 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS E 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR D 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N GLN E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR E 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL G 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA E 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU G 57 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS E 58 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR G 59 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 71 removed outlier: 5.761A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL C 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL D 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL E 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY D 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 77 through 82 removed outlier: 6.576A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR B 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS A 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 94 132 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 639 1.28 - 1.35: 559 1.35 - 1.42: 100 1.42 - 1.48: 594 1.48 - 1.55: 1611 Bond restraints: 3503 Sorted by residual: bond pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.18e-02 7.18e+03 3.06e+00 bond pdb=" C SER A 87 " pdb=" O SER A 87 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.20e-02 6.94e+03 2.83e+00 bond pdb=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.234 1.216 0.019 1.15e-02 7.56e+03 2.71e+00 bond pdb=" CA VAL A 82 " pdb=" CB VAL A 82 " ideal model delta sigma weight residual 1.544 1.521 0.023 1.42e-02 4.96e+03 2.62e+00 bond pdb=" C GLU A 83 " pdb=" O GLU A 83 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.30e-02 5.92e+03 2.47e+00 ... (remaining 3498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 4496 1.48 - 2.96: 225 2.96 - 4.45: 27 4.45 - 5.93: 1 5.93 - 7.41: 1 Bond angle restraints: 4750 Sorted by residual: angle pdb=" N GLU G 61 " pdb=" CA GLU G 61 " pdb=" C GLU G 61 " ideal model delta sigma weight residual 108.48 115.89 -7.41 1.80e+00 3.09e-01 1.70e+01 angle pdb=" C ASN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 122.66 119.83 2.83 9.70e-01 1.06e+00 8.50e+00 angle pdb=" N VAL B 74 " pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 106.85 110.70 -3.85 1.42e+00 4.96e-01 7.35e+00 angle pdb=" N THR B 75 " pdb=" CA THR B 75 " pdb=" C THR B 75 " ideal model delta sigma weight residual 110.91 114.07 -3.16 1.17e+00 7.31e-01 7.30e+00 angle pdb=" N THR C 75 " pdb=" CA THR C 75 " pdb=" C THR C 75 " ideal model delta sigma weight residual 110.91 113.96 -3.05 1.17e+00 7.31e-01 6.80e+00 ... (remaining 4745 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.94: 1723 15.94 - 31.88: 207 31.88 - 47.82: 51 47.82 - 63.76: 28 63.76 - 79.69: 7 Dihedral angle restraints: 2016 sinusoidal: 621 harmonic: 1395 Sorted by residual: dihedral pdb=" CA VAL L 74 " pdb=" C VAL L 74 " pdb=" N THR L 75 " pdb=" CA THR L 75 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA VAL I 74 " pdb=" C VAL I 74 " pdb=" N THR I 75 " pdb=" CA THR I 75 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL K 74 " pdb=" C VAL K 74 " pdb=" N THR K 75 " pdb=" CA THR K 75 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 517 0.072 - 0.143: 115 0.143 - 0.215: 2 0.215 - 0.286: 1 0.286 - 0.358: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" CA GLU A 83 " pdb=" N GLU A 83 " pdb=" C GLU A 83 " pdb=" CB GLU A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA VAL A 82 " pdb=" N VAL A 82 " pdb=" C VAL A 82 " pdb=" CB VAL A 82 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 633 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 81 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR A 81 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 81 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 82 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 75 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C THR G 75 " 0.024 2.00e-02 2.50e+03 pdb=" O THR G 75 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA G 76 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 75 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C THR E 75 " -0.024 2.00e-02 2.50e+03 pdb=" O THR E 75 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA E 76 " 0.008 2.00e-02 2.50e+03 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 38 2.49 - 3.09: 2422 3.09 - 3.69: 5188 3.69 - 4.30: 7241 4.30 - 4.90: 13598 Nonbonded interactions: 28487 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" OG SER B 87 " model vdw 1.884 3.040 nonbonded pdb=" OG1 THR K 72 " pdb=" O THR L 72 " model vdw 2.046 3.040 nonbonded pdb=" OG1 THR I 72 " pdb=" O THR J 72 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR J 72 " pdb=" O THR K 72 " model vdw 2.148 3.040 nonbonded pdb=" NE2 HIS D 50 " pdb=" OE2 GLU E 83 " model vdw 2.165 3.120 ... (remaining 28482 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.840 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3503 Z= 0.207 Angle : 0.716 7.411 4750 Z= 0.448 Chirality : 0.053 0.358 636 Planarity : 0.003 0.022 605 Dihedral : 17.463 79.693 1134 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 31.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 18.58 % Allowed : 26.55 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.15 (0.25), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3503) covalent geometry : angle 0.71622 ( 4750) hydrogen bonds : bond 0.23744 ( 132) hydrogen bonds : angle 10.62755 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 91 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: F 96 LYS cc_start: 0.8518 (tttt) cc_final: 0.8093 (tppt) REVERT: H 88 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7554 (mt) REVERT: H 96 LYS cc_start: 0.8570 (tttt) cc_final: 0.8296 (ttmm) REVERT: K 64 THR cc_start: 0.8045 (t) cc_final: 0.7838 (p) outliers start: 63 outliers final: 34 residues processed: 142 average time/residue: 0.0599 time to fit residues: 10.5085 Evaluate side-chains 107 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN C 62 GLN C 65 ASN D 65 ASN K 65 ASN E 65 ASN G 50 HIS G 65 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.137110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.117553 restraints weight = 6713.001| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.72 r_work: 0.3966 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3503 Z= 0.165 Angle : 0.628 5.004 4750 Z= 0.366 Chirality : 0.049 0.145 636 Planarity : 0.003 0.016 605 Dihedral : 9.699 59.467 557 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 16.22 % Allowed : 28.91 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.94 (0.25), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE J 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3503) covalent geometry : angle 0.62850 ( 4750) hydrogen bonds : bond 0.04533 ( 132) hydrogen bonds : angle 7.11660 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 95 time to evaluate : 0.138 Fit side-chains REVERT: F 96 LYS cc_start: 0.8924 (tttt) cc_final: 0.8191 (tppt) REVERT: H 96 LYS cc_start: 0.8842 (tttt) cc_final: 0.8384 (ttmm) outliers start: 55 outliers final: 26 residues processed: 139 average time/residue: 0.0642 time to fit residues: 11.0199 Evaluate side-chains 98 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN J 65 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.132970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.114096 restraints weight = 6886.558| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.70 r_work: 0.3920 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3503 Z= 0.217 Angle : 0.654 4.868 4750 Z= 0.379 Chirality : 0.050 0.157 636 Planarity : 0.003 0.016 605 Dihedral : 9.180 58.012 532 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 32.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 13.86 % Allowed : 28.91 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.26), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.003 PHE J 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 3503) covalent geometry : angle 0.65440 ( 4750) hydrogen bonds : bond 0.03649 ( 132) hydrogen bonds : angle 6.93066 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 0.127 Fit side-chains REVERT: F 96 LYS cc_start: 0.8841 (tttt) cc_final: 0.8213 (tppt) REVERT: H 96 LYS cc_start: 0.8872 (tttt) cc_final: 0.8441 (ttmm) REVERT: G 61 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6508 (tp30) outliers start: 47 outliers final: 30 residues processed: 119 average time/residue: 0.0576 time to fit residues: 8.5540 Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN G 65 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.117446 restraints weight = 6753.751| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.79 r_work: 0.3969 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3503 Z= 0.162 Angle : 0.607 4.547 4750 Z= 0.350 Chirality : 0.049 0.147 636 Planarity : 0.003 0.015 605 Dihedral : 8.238 58.565 530 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 27.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 12.98 % Allowed : 27.14 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE J 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3503) covalent geometry : angle 0.60735 ( 4750) hydrogen bonds : bond 0.03181 ( 132) hydrogen bonds : angle 6.51844 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 0.122 Fit side-chains REVERT: F 96 LYS cc_start: 0.8838 (tttt) cc_final: 0.8221 (tppt) REVERT: A 62 GLN cc_start: 0.5959 (mp10) cc_final: 0.5695 (mp10) REVERT: H 96 LYS cc_start: 0.8877 (tttt) cc_final: 0.8455 (ttmm) REVERT: E 83 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7996 (tp30) REVERT: G 61 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6399 (tp30) outliers start: 44 outliers final: 27 residues processed: 117 average time/residue: 0.0520 time to fit residues: 7.6327 Evaluate side-chains 99 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.130594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.112212 restraints weight = 6918.311| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.66 r_work: 0.3892 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 3503 Z= 0.252 Angle : 0.675 5.561 4750 Z= 0.387 Chirality : 0.049 0.137 636 Planarity : 0.003 0.018 605 Dihedral : 8.385 56.166 527 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 31.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 13.86 % Allowed : 25.66 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE J 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 3503) covalent geometry : angle 0.67452 ( 4750) hydrogen bonds : bond 0.03248 ( 132) hydrogen bonds : angle 6.87275 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 73 time to evaluate : 0.135 Fit side-chains REVERT: F 94 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6193 (t80) REVERT: F 96 LYS cc_start: 0.8848 (tttt) cc_final: 0.8275 (tppt) REVERT: A 83 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5117 (mt-10) REVERT: H 96 LYS cc_start: 0.8936 (tttt) cc_final: 0.8470 (ttmm) REVERT: G 61 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6287 (tp30) outliers start: 47 outliers final: 30 residues processed: 110 average time/residue: 0.0560 time to fit residues: 7.8127 Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.136535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.117887 restraints weight = 6775.532| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.71 r_work: 0.3977 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3503 Z= 0.166 Angle : 0.602 4.014 4750 Z= 0.347 Chirality : 0.049 0.194 636 Planarity : 0.003 0.016 605 Dihedral : 7.467 53.667 526 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 11.50 % Allowed : 28.32 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE J 94 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3503) covalent geometry : angle 0.60196 ( 4750) hydrogen bonds : bond 0.03017 ( 132) hydrogen bonds : angle 6.47504 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 78 time to evaluate : 0.128 Fit side-chains REVERT: F 96 LYS cc_start: 0.8783 (tttt) cc_final: 0.8264 (tppt) REVERT: A 83 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5338 (mt-10) REVERT: A 87 SER cc_start: 0.8767 (p) cc_final: 0.8445 (t) REVERT: H 96 LYS cc_start: 0.8884 (tttt) cc_final: 0.8455 (ttmm) REVERT: I 61 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6500 (tm-30) outliers start: 39 outliers final: 25 residues processed: 106 average time/residue: 0.0528 time to fit residues: 7.2064 Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.130986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112761 restraints weight = 6986.312| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.64 r_work: 0.3897 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3503 Z= 0.240 Angle : 0.673 5.571 4750 Z= 0.386 Chirality : 0.048 0.144 636 Planarity : 0.003 0.019 605 Dihedral : 7.805 56.398 525 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 10.91 % Allowed : 33.04 % Favored : 56.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE J 94 HIS 0.005 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 3503) covalent geometry : angle 0.67302 ( 4750) hydrogen bonds : bond 0.03281 ( 132) hydrogen bonds : angle 6.71801 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.127 Fit side-chains REVERT: F 94 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6180 (t80) REVERT: F 96 LYS cc_start: 0.8804 (tttt) cc_final: 0.8319 (tppt) REVERT: A 83 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5160 (mt-10) REVERT: A 87 SER cc_start: 0.8845 (p) cc_final: 0.8551 (t) REVERT: H 96 LYS cc_start: 0.8907 (tttt) cc_final: 0.8455 (ttmm) REVERT: I 61 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: C 61 GLU cc_start: 0.7247 (tt0) cc_final: 0.7039 (tt0) REVERT: E 57 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: G 61 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6269 (tp30) outliers start: 37 outliers final: 25 residues processed: 97 average time/residue: 0.0609 time to fit residues: 7.4376 Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 32 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.0060 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.139751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.120982 restraints weight = 6844.047| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.75 r_work: 0.4034 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3503 Z= 0.146 Angle : 0.607 5.116 4750 Z= 0.346 Chirality : 0.048 0.168 636 Planarity : 0.003 0.019 605 Dihedral : 7.086 54.987 525 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 7.08 % Allowed : 37.46 % Favored : 55.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE J 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3503) covalent geometry : angle 0.60669 ( 4750) hydrogen bonds : bond 0.02847 ( 132) hydrogen bonds : angle 6.21977 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.134 Fit side-chains REVERT: F 96 LYS cc_start: 0.8742 (tttt) cc_final: 0.8319 (tppt) REVERT: A 87 SER cc_start: 0.8583 (p) cc_final: 0.8330 (t) REVERT: H 96 LYS cc_start: 0.8845 (tttt) cc_final: 0.8430 (ttmm) REVERT: I 61 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6691 (tm-30) outliers start: 24 outliers final: 21 residues processed: 97 average time/residue: 0.0563 time to fit residues: 6.9478 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.140392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.121928 restraints weight = 6703.537| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 3.68 r_work: 0.4034 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3503 Z= 0.153 Angle : 0.607 4.643 4750 Z= 0.349 Chirality : 0.048 0.176 636 Planarity : 0.003 0.019 605 Dihedral : 6.504 42.412 522 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 7.08 % Allowed : 39.82 % Favored : 53.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE J 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3503) covalent geometry : angle 0.60681 ( 4750) hydrogen bonds : bond 0.02760 ( 132) hydrogen bonds : angle 6.11388 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.136 Fit side-chains REVERT: F 94 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6211 (t80) REVERT: F 96 LYS cc_start: 0.8743 (tttt) cc_final: 0.8335 (tppt) REVERT: A 87 SER cc_start: 0.8568 (p) cc_final: 0.8325 (t) REVERT: H 96 LYS cc_start: 0.8807 (tttt) cc_final: 0.8403 (ttmm) REVERT: I 61 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: E 57 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: G 61 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6157 (tp30) outliers start: 24 outliers final: 19 residues processed: 87 average time/residue: 0.0575 time to fit residues: 6.2525 Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.136604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.118367 restraints weight = 6865.584| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.64 r_work: 0.3980 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3503 Z= 0.195 Angle : 0.631 4.884 4750 Z= 0.362 Chirality : 0.048 0.160 636 Planarity : 0.003 0.020 605 Dihedral : 6.823 44.422 521 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 7.08 % Allowed : 39.82 % Favored : 53.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE J 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3503) covalent geometry : angle 0.63053 ( 4750) hydrogen bonds : bond 0.02827 ( 132) hydrogen bonds : angle 6.34265 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.139 Fit side-chains REVERT: F 94 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6231 (t80) REVERT: F 96 LYS cc_start: 0.8760 (tttt) cc_final: 0.8371 (tppt) REVERT: A 87 SER cc_start: 0.8674 (p) cc_final: 0.8448 (t) REVERT: H 96 LYS cc_start: 0.8868 (tttt) cc_final: 0.8451 (ttmm) REVERT: I 61 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: E 57 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: G 61 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6205 (tp30) outliers start: 24 outliers final: 18 residues processed: 83 average time/residue: 0.0552 time to fit residues: 5.8525 Evaluate side-chains 83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.136416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.118241 restraints weight = 6825.945| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.60 r_work: 0.3986 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3503 Z= 0.191 Angle : 0.620 4.726 4750 Z= 0.356 Chirality : 0.048 0.161 636 Planarity : 0.003 0.020 605 Dihedral : 6.839 44.934 521 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 8.26 % Allowed : 38.64 % Favored : 53.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE J 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3503) covalent geometry : angle 0.62006 ( 4750) hydrogen bonds : bond 0.02775 ( 132) hydrogen bonds : angle 6.36725 ( 393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 901.13 seconds wall clock time: 16 minutes 20.62 seconds (980.62 seconds total)