Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:45:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_23270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_23270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_23270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_23270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc9_23270/11_2022/7lc9_23270.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/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: 2.34, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 1.43 Conformation dependent library (CDL) restraints added in 572.3 milliseconds 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: 0.24 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: 0.85 Time building geometry restraints manager: 1.54 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: 105.22 - 110.42: 904 110.42 - 115.62: 1510 115.62 - 120.81: 1156 120.81 - 126.01: 1174 126.01 - 131.21: 6 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 2.440 nonbonded pdb=" OG1 THR K 72 " pdb=" O THR L 72 " model vdw 2.046 2.440 nonbonded pdb=" OG1 THR I 72 " pdb=" O THR J 72 " model vdw 2.146 2.440 nonbonded pdb=" OG1 THR J 72 " pdb=" O THR K 72 " model vdw 2.148 2.440 nonbonded pdb=" NE2 HIS D 50 " pdb=" OE2 GLU E 83 " model vdw 2.165 2.520 ... (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 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 3.580 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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= 0.262 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.25), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.19), residues: 501 *********************** 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 fitting. rotamer outliers: 63 poor density : 91 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 34 residues processed: 142 average time/residue: 0.1449 time to fit residues: 25.2372 Evaluate side-chains 106 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.0523 time to fit residues: 3.2164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3503 Z= 0.296 Angle : 0.653 4.945 4750 Z= 0.378 Chirality : 0.048 0.143 636 Planarity : 0.003 0.016 605 Dihedral : 6.261 24.238 513 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 35.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer Outliers : 9.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.26), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.19), residues: 501 *********************** 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 119 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.439 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 117 average time/residue: 0.1305 time to fit residues: 19.1003 Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0550 time to fit residues: 1.6512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 14 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 3503 Z= 0.256 Angle : 0.619 4.447 4750 Z= 0.357 Chirality : 0.049 0.158 636 Planarity : 0.003 0.015 605 Dihedral : 6.089 29.410 513 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 32.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer Outliers : 8.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 501 *********************** 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 115 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.366 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 111 average time/residue: 0.1268 time to fit residues: 17.6023 Evaluate side-chains 83 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0368 time to fit residues: 1.2094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 3503 Z= 0.394 Angle : 0.684 5.413 4750 Z= 0.393 Chirality : 0.050 0.163 636 Planarity : 0.003 0.017 605 Dihedral : 6.611 28.118 513 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 35.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer Outliers : 8.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.21), residues: 501 *********************** 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 109 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.411 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 100 average time/residue: 0.1454 time to fit residues: 17.8589 Evaluate side-chains 80 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0626 time to fit residues: 1.3042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3503 Z= 0.226 Angle : 0.612 4.338 4750 Z= 0.352 Chirality : 0.048 0.143 636 Planarity : 0.003 0.016 605 Dihedral : 5.884 31.354 513 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 6.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 501 *********************** 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 105 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.389 Fit side-chains outliers start: 22 outliers final: 6 residues processed: 100 average time/residue: 0.1365 time to fit residues: 16.9358 Evaluate side-chains 75 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0341 time to fit residues: 0.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3503 Z= 0.275 Angle : 0.614 4.081 4750 Z= 0.352 Chirality : 0.048 0.145 636 Planarity : 0.003 0.018 605 Dihedral : 5.899 30.006 513 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 31.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer Outliers : 5.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 501 *********************** 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 92 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.420 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.1242 time to fit residues: 13.7580 Evaluate side-chains 74 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0775 time to fit residues: 1.4141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3552 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= 0.263 Angle : 0.616 4.529 4750 Z= 0.354 Chirality : 0.047 0.139 636 Planarity : 0.003 0.018 605 Dihedral : 5.857 29.876 513 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 32.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer Outliers : 4.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 501 *********************** 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 91 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.411 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1404 time to fit residues: 15.1173 Evaluate side-chains 80 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0620 time to fit residues: 1.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3557 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= 0.338 Angle : 0.656 4.776 4750 Z= 0.374 Chirality : 0.048 0.136 636 Planarity : 0.003 0.019 605 Dihedral : 6.096 29.061 513 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 34.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.21), residues: 501 *********************** 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 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.440 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 83 average time/residue: 0.1469 time to fit residues: 15.0903 Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1075 time to fit residues: 1.0405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3503 Z= 0.272 Angle : 0.636 5.204 4750 Z= 0.361 Chirality : 0.048 0.142 636 Planarity : 0.003 0.019 605 Dihedral : 5.932 30.016 513 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 501 *********************** 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 79 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.413 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.1464 time to fit residues: 14.0985 Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1008 time to fit residues: 0.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 3503 Z= 0.338 Angle : 0.666 5.552 4750 Z= 0.378 Chirality : 0.048 0.139 636 Planarity : 0.003 0.020 605 Dihedral : 6.112 29.828 513 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 35.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.97 % Favored : 87.03 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.28), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.21), residues: 501 ********************** 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 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.432 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.1479 time to fit residues: 12.7701 Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3197 time to fit residues: 0.8660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** 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 = 0.4306 r_free = 0.4306 target = 0.126473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.108762 restraints weight = 7081.246| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 3.53 r_work: 0.3960 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work: 0.3941 rms_B_bonded: 3.30 restraints_weight: 0.1250 r_work: 0.3931 rms_B_bonded: 3.38 restraints_weight: 0.0625 r_work: 0.3921 rms_B_bonded: 3.49 restraints_weight: 0.0312 r_work: 0.3910 rms_B_bonded: 3.62 restraints_weight: 0.0156 r_work: 0.3898 rms_B_bonded: 3.78 restraints_weight: 0.0078 r_work: 0.3886 rms_B_bonded: 3.97 restraints_weight: 0.0039 r_work: 0.3874 rms_B_bonded: 4.18 restraints_weight: 0.0020 r_work: 0.3861 rms_B_bonded: 4.42 restraints_weight: 0.0010 r_work: 0.3848 rms_B_bonded: 4.68 restraints_weight: 0.0005 r_work: 0.3834 rms_B_bonded: 4.98 restraints_weight: 0.0002 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.088 3503 Z= 0.613 Angle : 0.867 8.711 4750 Z= 0.485 Chirality : 0.052 0.194 636 Planarity : 0.004 0.021 605 Dihedral : 7.264 28.197 513 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 46.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.27), residues: 501 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 501 =============================================================================== Job complete usr+sys time: 1153.38 seconds wall clock time: 21 minutes 59.82 seconds (1319.82 seconds total)