Starting phenix.real_space_refine on Thu Dec 7 19:46:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/12_2023/6osl_20185.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 2540 2.51 5 N 710 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "B" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "D" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "F" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "H" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "I" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 2.36, per 1000 atoms: 0.58 Number of scatterers: 4060 At special positions: 0 Unit cell: (98.58, 83.74, 42.4, 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 810 8.00 N 710 7.00 C 2540 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: 1.45 Conformation dependent library (CDL) restraints added in 973.9 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.706A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 7.313A pdb=" N GLU C 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY A 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU E 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL G 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU I 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY G 47 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.527A pdb=" N VAL E 52 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL G 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 65 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N THR I 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL G 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL I 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY G 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA I 76 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS I 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N GLN G 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.313A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU F 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU F 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL H 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU J 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.498A pdb=" N VAL B 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL H 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 75 removed outlier: 8.967A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N VAL D 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY B 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N THR F 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL D 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY D 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N THR H 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL F 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL H 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLY F 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ALA H 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N THR J 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL H 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL J 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY H 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.809A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.522A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL H 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 95 hydrogen bonds defined for protein. 279 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: 1.03 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 700 1.28 - 1.35: 630 1.35 - 1.42: 180 1.42 - 1.48: 701 1.48 - 1.55: 1869 Bond restraints: 4080 Sorted by residual: bond pdb=" CB GLU I 57 " pdb=" CG GLU I 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB GLU H 57 " pdb=" CG GLU H 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU D 57 " pdb=" CG GLU D 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU C 57 " pdb=" CG GLU C 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 106.12 - 111.05: 1822 111.05 - 115.99: 1053 115.99 - 120.92: 1341 120.92 - 125.85: 1284 125.85 - 130.79: 10 Bond angle restraints: 5510 Sorted by residual: angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 122.46 113.24 9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL I 49 " pdb=" N HIS I 50 " pdb=" CA HIS I 50 " ideal model delta sigma weight residual 122.46 113.28 9.18 1.80e+00 3.09e-01 2.60e+01 ... (remaining 5505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 2200 16.33 - 32.65: 159 32.65 - 48.97: 11 48.97 - 65.29: 0 65.29 - 81.62: 10 Dihedral angle restraints: 2380 sinusoidal: 790 harmonic: 1590 Sorted by residual: dihedral pdb=" CA THR D 75 " pdb=" C THR D 75 " pdb=" N ALA D 76 " pdb=" CA ALA D 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR J 75 " pdb=" C THR J 75 " pdb=" N ALA J 76 " pdb=" CA ALA J 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR G 75 " pdb=" C THR G 75 " pdb=" N ALA G 76 " pdb=" CA ALA G 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 490 0.062 - 0.123: 187 0.123 - 0.185: 33 0.185 - 0.246: 0 0.246 - 0.308: 10 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS B 50 " pdb=" N HIS B 50 " pdb=" C HIS B 50 " pdb=" CB HIS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 717 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 50 " 0.020 2.00e-02 2.50e+03 1.81e-02 4.90e+00 pdb=" CG HIS H 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS H 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " 0.020 2.00e-02 2.50e+03 1.79e-02 4.82e+00 pdb=" CG HIS F 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.019 2.00e-02 2.50e+03 1.79e-02 4.80e+00 pdb=" CG HIS B 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1390 2.83 - 3.34: 3595 3.34 - 3.86: 6312 3.86 - 4.38: 6929 4.38 - 4.90: 14282 Nonbonded interactions: 32508 Sorted by model distance: nonbonded pdb=" O HIS B 50 " pdb=" O GLY D 51 " model vdw 2.308 3.040 nonbonded pdb=" O HIS E 50 " pdb=" O GLY G 51 " model vdw 2.367 3.040 nonbonded pdb=" O HIS F 50 " pdb=" O GLY H 51 " model vdw 2.385 3.040 nonbonded pdb=" O HIS C 50 " pdb=" O GLY E 51 " model vdw 2.392 3.040 nonbonded pdb=" O HIS G 50 " pdb=" O GLY I 51 " model vdw 2.397 3.040 ... (remaining 32503 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 1.890 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.010 0.044 4080 Z= 0.699 Angle : 1.064 9.216 5510 Z= 0.629 Chirality : 0.074 0.308 720 Planarity : 0.004 0.018 680 Dihedral : 13.469 81.616 1380 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.44 % Allowed : 16.83 % Favored : 80.73 % 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: -4.40 (0.22), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.010 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.006 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.438 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 1.1362 time to fit residues: 112.6869 Evaluate side-chains 48 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 4080 Z= 0.137 Angle : 0.592 6.830 5510 Z= 0.355 Chirality : 0.056 0.199 720 Planarity : 0.003 0.015 680 Dihedral : 4.865 15.445 590 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.85 % Allowed : 24.88 % Favored : 69.27 % 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: -3.75 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.006 HIS H 50 PHE 0.024 0.003 PHE E 94 TYR 0.002 0.000 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.465 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 78 average time/residue: 0.6857 time to fit residues: 56.4948 Evaluate side-chains 54 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 7 average time/residue: 0.2625 time to fit residues: 2.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4080 Z= 0.371 Angle : 0.766 7.418 5510 Z= 0.456 Chirality : 0.060 0.265 720 Planarity : 0.004 0.016 680 Dihedral : 5.682 15.695 590 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 10.98 % Allowed : 22.20 % Favored : 66.83 % 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: -3.67 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.008 HIS C 50 PHE 0.020 0.003 PHE C 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 49 time to evaluate : 0.442 Fit side-chains outliers start: 45 outliers final: 33 residues processed: 74 average time/residue: 0.7424 time to fit residues: 57.9038 Evaluate side-chains 77 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 44 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 19 residues processed: 14 average time/residue: 0.4690 time to fit residues: 7.5825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4080 Z= 0.273 Angle : 0.675 6.758 5510 Z= 0.404 Chirality : 0.057 0.237 720 Planarity : 0.003 0.016 680 Dihedral : 5.327 15.171 590 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 13.41 % Allowed : 21.22 % Favored : 65.37 % 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: -3.51 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.023 0.003 PHE D 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 53 time to evaluate : 0.452 Fit side-chains outliers start: 55 outliers final: 43 residues processed: 87 average time/residue: 0.6368 time to fit residues: 58.8390 Evaluate side-chains 90 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 47 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 28 residues processed: 15 average time/residue: 0.2665 time to fit residues: 5.0466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 4080 Z= 0.560 Angle : 0.887 8.051 5510 Z= 0.528 Chirality : 0.065 0.286 720 Planarity : 0.004 0.020 680 Dihedral : 6.178 17.359 590 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 13.41 % Allowed : 22.93 % Favored : 63.66 % 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: -3.68 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.009 HIS C 50 PHE 0.018 0.003 PHE I 94 TYR 0.011 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 44 time to evaluate : 0.400 Fit side-chains outliers start: 55 outliers final: 42 residues processed: 82 average time/residue: 0.6970 time to fit residues: 60.3787 Evaluate side-chains 82 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 40 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 31 residues processed: 11 average time/residue: 0.1767 time to fit residues: 2.8258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.003 0.014 4080 Z= 0.183 Angle : 0.610 6.520 5510 Z= 0.365 Chirality : 0.054 0.211 720 Planarity : 0.003 0.018 680 Dihedral : 5.031 17.061 590 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 10.49 % Allowed : 25.61 % Favored : 63.90 % 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: -3.44 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.011 0.002 PHE D 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 51 time to evaluate : 0.452 Fit side-chains outliers start: 43 outliers final: 36 residues processed: 80 average time/residue: 0.5704 time to fit residues: 49.0592 Evaluate side-chains 82 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 46 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 25 residues processed: 11 average time/residue: 0.2131 time to fit residues: 3.3446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4080 Z= 0.330 Angle : 0.726 7.339 5510 Z= 0.433 Chirality : 0.058 0.253 720 Planarity : 0.003 0.018 680 Dihedral : 5.469 15.082 590 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 11.95 % Allowed : 23.66 % Favored : 64.39 % 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: -3.48 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.008 HIS F 50 PHE 0.018 0.003 PHE D 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 46 time to evaluate : 0.332 Fit side-chains outliers start: 49 outliers final: 42 residues processed: 77 average time/residue: 0.4814 time to fit residues: 39.4784 Evaluate side-chains 87 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 45 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 15 average time/residue: 0.2979 time to fit residues: 5.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4080 Z= 0.194 Angle : 0.620 6.633 5510 Z= 0.371 Chirality : 0.054 0.218 720 Planarity : 0.003 0.017 680 Dihedral : 4.992 16.880 590 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 8.05 % Allowed : 28.54 % Favored : 63.41 % 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: -3.33 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.006 HIS F 50 PHE 0.024 0.002 PHE D 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 53 time to evaluate : 0.455 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 30 residues processed: 80 average time/residue: 0.5930 time to fit residues: 50.7058 Evaluate side-chains 77 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 47 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.9578 time to fit residues: 4.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4080 Z= 0.148 Angle : 0.573 6.030 5510 Z= 0.343 Chirality : 0.054 0.203 720 Planarity : 0.003 0.016 680 Dihedral : 4.664 17.209 590 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 8.29 % Allowed : 27.80 % Favored : 63.90 % 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: -3.18 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS H 50 PHE 0.023 0.002 PHE D 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 60 time to evaluate : 0.400 Fit side-chains outliers start: 34 outliers final: 30 residues processed: 85 average time/residue: 0.5815 time to fit residues: 52.7118 Evaluate side-chains 85 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.2977 time to fit residues: 2.5477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4080 Z= 0.271 Angle : 0.689 7.584 5510 Z= 0.412 Chirality : 0.056 0.246 720 Planarity : 0.003 0.017 680 Dihedral : 5.235 20.004 590 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 7.32 % Allowed : 27.32 % Favored : 65.37 % 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: -3.23 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.007 HIS F 50 PHE 0.022 0.002 PHE D 94 TYR 0.004 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 0.429 Fit side-chains outliers start: 30 outliers final: 27 residues processed: 78 average time/residue: 0.5958 time to fit residues: 49.5947 Evaluate side-chains 79 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 52 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 0.5429 time to fit residues: 2.2792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.2980 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.200127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.171680 restraints weight = 4562.093| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 2.60 r_work: 0.4373 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4080 Z= 0.323 Angle : 0.732 7.742 5510 Z= 0.437 Chirality : 0.058 0.257 720 Planarity : 0.003 0.016 680 Dihedral : 5.488 22.909 590 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 7.56 % Allowed : 28.05 % Favored : 64.39 % 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: -3.35 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.008 HIS D 50 PHE 0.020 0.002 PHE D 94 TYR 0.005 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.18 seconds wall clock time: 33 minutes 24.93 seconds (2004.93 seconds total)