Starting phenix.real_space_refine on Sun Mar 10 20:43:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sst_10305/03_2024/6sst_10305.pdb" } resolution = 3.4 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= 0.002 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 3050 2.51 5 N 860 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.03, per 1000 atoms: 0.62 Number of scatterers: 4900 At special positions: 0 Unit cell: (97.495, 122.655, 44.03, 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 990 8.00 N 860 7.00 C 3050 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: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 56.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 49 removed outlier: 6.861A pdb=" N LEU B 38 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR A 39 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER B 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A 43 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.575A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL C 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N VAL D 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 91 removed outlier: 6.491A pdb=" N SER A 87 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ALA D 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER D 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 15 through 23 Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 49 removed outlier: 6.823A pdb=" N LEU G 38 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR F 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 40 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY F 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER G 42 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS F 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR G 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS F 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU G 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL H 37 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N VAL I 40 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N VAL I 37 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N VAL J 40 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 52 through 57 Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB3, first strand: chain 'F' and resid 69 through 71 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 91 removed outlier: 6.496A pdb=" N SER F 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA G 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA F 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER G 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA H 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA G 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER H 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA I 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 198 hydrogen bonds defined for protein. 594 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: 1.32 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 870 1.29 - 1.35: 770 1.35 - 1.41: 177 1.41 - 1.48: 833 1.48 - 1.54: 2260 Bond restraints: 4910 Sorted by residual: bond pdb=" CB THR D 44 " pdb=" CG2 THR D 44 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB THR I 44 " pdb=" CG2 THR I 44 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CB THR C 44 " pdb=" CG2 THR C 44 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CB THR H 44 " pdb=" CG2 THR H 44 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR A 44 " pdb=" CG2 THR A 44 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 ... (remaining 4905 not shown) Histogram of bond angle deviations from ideal: 105.42 - 110.62: 1599 110.62 - 115.81: 1741 115.81 - 121.01: 1745 121.01 - 126.21: 1525 126.21 - 131.40: 20 Bond angle restraints: 6630 Sorted by residual: angle pdb=" C GLY C 84 " pdb=" N ALA C 85 " pdb=" CA ALA C 85 " ideal model delta sigma weight residual 122.68 126.37 -3.69 1.47e+00 4.63e-01 6.30e+00 angle pdb=" C GLY D 84 " pdb=" N ALA D 85 " pdb=" CA ALA D 85 " ideal model delta sigma weight residual 122.68 126.35 -3.67 1.47e+00 4.63e-01 6.23e+00 angle pdb=" C GLY F 84 " pdb=" N ALA F 85 " pdb=" CA ALA F 85 " ideal model delta sigma weight residual 122.68 126.35 -3.67 1.47e+00 4.63e-01 6.22e+00 angle pdb=" C GLY J 84 " pdb=" N ALA J 85 " pdb=" CA ALA J 85 " ideal model delta sigma weight residual 122.68 126.34 -3.66 1.47e+00 4.63e-01 6.20e+00 angle pdb=" C GLY I 84 " pdb=" N ALA I 85 " pdb=" CA ALA I 85 " ideal model delta sigma weight residual 122.68 126.34 -3.66 1.47e+00 4.63e-01 6.20e+00 ... (remaining 6625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2530 17.13 - 34.27: 230 34.27 - 51.40: 40 51.40 - 68.53: 30 68.53 - 85.66: 10 Dihedral angle restraints: 2840 sinusoidal: 900 harmonic: 1940 Sorted by residual: dihedral pdb=" CA GLY F 73 " pdb=" C GLY F 73 " pdb=" N VAL F 74 " pdb=" CA VAL F 74 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLY D 73 " pdb=" C GLY D 73 " pdb=" N VAL D 74 " pdb=" CA VAL D 74 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLY G 73 " pdb=" C GLY G 73 " pdb=" N VAL G 74 " pdb=" CA VAL G 74 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 506 0.048 - 0.095: 218 0.095 - 0.142: 136 0.142 - 0.190: 0 0.190 - 0.237: 10 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB THR C 44 " pdb=" CA THR C 44 " pdb=" OG1 THR C 44 " pdb=" CG2 THR C 44 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR F 44 " pdb=" CA THR F 44 " pdb=" OG1 THR F 44 " pdb=" CG2 THR F 44 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR D 44 " pdb=" CA THR D 44 " pdb=" OG1 THR D 44 " pdb=" CG2 THR D 44 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 867 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 58 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LYS F 58 " 0.023 2.00e-02 2.50e+03 pdb=" O LYS F 58 " -0.009 2.00e-02 2.50e+03 pdb=" N THR F 59 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 58 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LYS H 58 " 0.022 2.00e-02 2.50e+03 pdb=" O LYS H 58 " -0.009 2.00e-02 2.50e+03 pdb=" N THR H 59 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 58 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C LYS I 58 " 0.022 2.00e-02 2.50e+03 pdb=" O LYS I 58 " -0.009 2.00e-02 2.50e+03 pdb=" N THR I 59 " -0.007 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2136 2.92 - 3.42: 4158 3.42 - 3.91: 8392 3.91 - 4.41: 8896 4.41 - 4.90: 17858 Nonbonded interactions: 41440 Sorted by model distance: nonbonded pdb=" OE1 GLN D 62 " pdb=" NE2 GLN E 62 " model vdw 2.430 2.520 nonbonded pdb=" OE1 GLN F 62 " pdb=" NE2 GLN G 62 " model vdw 2.432 2.520 nonbonded pdb=" OE1 GLN A 62 " pdb=" NE2 GLN B 62 " model vdw 2.484 2.520 nonbonded pdb=" OE1 GLN I 62 " pdb=" NE2 GLN J 62 " model vdw 2.500 2.520 nonbonded pdb=" OE1 GLN G 62 " pdb=" NE2 GLN H 62 " model vdw 2.502 2.520 ... (remaining 41435 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.560 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.190 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.009 0.056 4910 Z= 0.598 Angle : 0.941 4.734 6630 Z= 0.559 Chirality : 0.065 0.237 870 Planarity : 0.004 0.013 830 Dihedral : 16.794 85.661 1620 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % 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: -4.47 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.003 0.001 PHE E 94 TYR 0.014 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 THR cc_start: 0.9387 (m) cc_final: 0.9186 (m) REVERT: C 58 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6738 (tptp) REVERT: C 83 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7414 (mt-10) REVERT: D 58 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7018 (tptp) REVERT: D 72 THR cc_start: 0.9573 (m) cc_final: 0.9343 (m) REVERT: E 58 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6859 (tptp) REVERT: G 83 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7046 (mt-10) REVERT: H 83 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7462 (mt-10) REVERT: I 58 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6478 (ttpt) REVERT: I 80 LYS cc_start: 0.8344 (mttp) cc_final: 0.7742 (mtpt) REVERT: J 58 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6998 (tppt) REVERT: J 80 LYS cc_start: 0.8610 (mttp) cc_final: 0.8397 (mttp) outliers start: 10 outliers final: 2 residues processed: 45 average time/residue: 0.2679 time to fit residues: 14.5990 Evaluate side-chains 35 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain J residue 58 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4910 Z= 0.188 Angle : 0.570 6.449 6630 Z= 0.329 Chirality : 0.053 0.125 870 Planarity : 0.002 0.009 830 Dihedral : 9.662 57.542 748 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 5.32 % Allowed : 9.57 % Favored : 85.11 % 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: -4.28 (0.28), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.001 PHE A 94 TYR 0.006 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 26 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 72 THR cc_start: 0.9340 (m) cc_final: 0.9094 (m) REVERT: C 83 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 58 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6715 (tptp) REVERT: D 72 THR cc_start: 0.9499 (m) cc_final: 0.9227 (m) REVERT: D 83 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7248 (mt-10) REVERT: E 58 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6847 (tptp) REVERT: F 83 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7312 (mt-10) REVERT: G 58 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6756 (tptp) REVERT: I 58 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6597 (tptp) REVERT: J 58 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6822 (tppt) outliers start: 25 outliers final: 7 residues processed: 50 average time/residue: 0.1727 time to fit residues: 11.3244 Evaluate side-chains 38 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain J residue 58 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4910 Z= 0.471 Angle : 0.667 5.405 6630 Z= 0.388 Chirality : 0.055 0.130 870 Planarity : 0.003 0.011 830 Dihedral : 8.369 58.261 740 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % Rotamer: Outliers : 4.47 % Allowed : 10.64 % Favored : 84.89 % 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: -4.58 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.006 0.001 PHE A 94 TYR 0.016 0.004 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 29 time to evaluate : 0.508 Fit side-chains REVERT: A 72 THR cc_start: 0.9475 (m) cc_final: 0.9251 (m) REVERT: C 83 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 72 THR cc_start: 0.9576 (m) cc_final: 0.9366 (m) REVERT: D 83 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7424 (mt-10) REVERT: F 61 GLU cc_start: 0.7776 (mp0) cc_final: 0.7112 (mp0) REVERT: F 72 THR cc_start: 0.9352 (m) cc_final: 0.9127 (m) REVERT: F 83 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7317 (mt-10) REVERT: G 58 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6755 (mmmt) REVERT: G 83 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7262 (mt-10) outliers start: 21 outliers final: 15 residues processed: 49 average time/residue: 0.1359 time to fit residues: 9.5460 Evaluate side-chains 41 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 4910 Z= 0.461 Angle : 0.654 5.483 6630 Z= 0.381 Chirality : 0.056 0.132 870 Planarity : 0.003 0.011 830 Dihedral : 7.195 52.567 724 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 5.11 % Allowed : 9.79 % Favored : 85.11 % 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: -4.90 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.006 0.001 PHE A 94 TYR 0.014 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 32 time to evaluate : 0.510 Fit side-chains REVERT: A 72 THR cc_start: 0.9500 (m) cc_final: 0.9215 (m) REVERT: B 83 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6646 (mt-10) REVERT: C 83 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6935 (mt-10) REVERT: D 83 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7420 (mt-10) REVERT: F 61 GLU cc_start: 0.7753 (mp0) cc_final: 0.7046 (mp0) REVERT: F 83 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6973 (mt-10) REVERT: G 58 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6694 (mmmt) REVERT: G 83 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7150 (mt-10) REVERT: H 83 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7487 (mp0) REVERT: J 58 LYS cc_start: 0.7654 (tttp) cc_final: 0.7109 (tptt) outliers start: 24 outliers final: 20 residues processed: 53 average time/residue: 0.1300 time to fit residues: 9.7593 Evaluate side-chains 50 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 29 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4910 Z= 0.176 Angle : 0.557 5.948 6630 Z= 0.322 Chirality : 0.053 0.123 870 Planarity : 0.002 0.013 830 Dihedral : 6.402 58.971 724 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 3.19 % Allowed : 12.55 % Favored : 84.26 % 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: -4.69 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.002 0.001 PHE A 94 TYR 0.003 0.000 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.9368 (m) cc_final: 0.9107 (m) REVERT: C 83 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7410 (mt-10) REVERT: D 83 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7423 (mt-10) REVERT: F 83 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7003 (mt-10) REVERT: G 83 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7099 (mt-10) REVERT: J 58 LYS cc_start: 0.7677 (tttp) cc_final: 0.7177 (tptt) outliers start: 15 outliers final: 11 residues processed: 41 average time/residue: 0.1274 time to fit residues: 7.6258 Evaluate side-chains 37 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4910 Z= 0.424 Angle : 0.620 5.151 6630 Z= 0.363 Chirality : 0.055 0.133 870 Planarity : 0.003 0.010 830 Dihedral : 6.447 21.474 720 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 3.40 % Allowed : 13.40 % Favored : 83.19 % 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: -4.93 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.005 0.001 PHE A 94 TYR 0.014 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.9470 (m) cc_final: 0.9189 (m) REVERT: C 83 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7481 (mt-10) REVERT: D 83 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7455 (mt-10) REVERT: F 72 THR cc_start: 0.9377 (m) cc_final: 0.9024 (m) REVERT: F 83 GLU cc_start: 0.7757 (mt-10) cc_final: 0.6917 (mt-10) REVERT: G 83 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7127 (mt-10) REVERT: H 83 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7201 (mp0) REVERT: I 58 LYS cc_start: 0.7646 (tttp) cc_final: 0.6832 (tptt) REVERT: J 58 LYS cc_start: 0.7754 (tttp) cc_final: 0.7201 (tptt) outliers start: 16 outliers final: 15 residues processed: 46 average time/residue: 0.1325 time to fit residues: 8.7189 Evaluate side-chains 51 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.0370 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4910 Z= 0.199 Angle : 0.554 5.493 6630 Z= 0.321 Chirality : 0.053 0.125 870 Planarity : 0.002 0.015 830 Dihedral : 6.011 21.075 720 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.62 % Allowed : 13.83 % Favored : 82.55 % 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: -4.77 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.002 0.001 PHE A 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 32 time to evaluate : 0.517 Fit side-chains REVERT: A 72 THR cc_start: 0.9366 (m) cc_final: 0.9093 (m) REVERT: C 83 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 58 LYS cc_start: 0.7467 (ttmp) cc_final: 0.6875 (tptt) REVERT: F 83 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6976 (mt-10) REVERT: G 83 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7104 (mt-10) REVERT: H 83 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7233 (mp0) REVERT: I 58 LYS cc_start: 0.7634 (tttp) cc_final: 0.6819 (tptt) REVERT: J 58 LYS cc_start: 0.7783 (tttp) cc_final: 0.7214 (tptt) outliers start: 17 outliers final: 13 residues processed: 46 average time/residue: 0.1461 time to fit residues: 9.4017 Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4910 Z= 0.487 Angle : 0.644 5.042 6630 Z= 0.377 Chirality : 0.056 0.134 870 Planarity : 0.003 0.014 830 Dihedral : 6.389 21.175 720 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Rotamer: Outliers : 3.83 % Allowed : 13.62 % Favored : 82.55 % 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: -4.99 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.005 0.001 PHE A 94 TYR 0.014 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.677 Fit side-chains REVERT: A 72 THR cc_start: 0.9472 (m) cc_final: 0.9197 (m) REVERT: B 83 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7401 (mp0) REVERT: D 83 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7484 (mt-10) REVERT: F 72 THR cc_start: 0.9378 (m) cc_final: 0.9023 (m) REVERT: F 83 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6919 (mt-10) REVERT: G 83 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7076 (mt-10) REVERT: H 83 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7241 (mp0) REVERT: I 58 LYS cc_start: 0.7630 (tttp) cc_final: 0.6774 (tptt) REVERT: J 58 LYS cc_start: 0.7795 (tttp) cc_final: 0.7188 (tptt) outliers start: 18 outliers final: 17 residues processed: 50 average time/residue: 0.1228 time to fit residues: 9.2074 Evaluate side-chains 56 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4910 Z= 0.172 Angle : 0.563 5.811 6630 Z= 0.324 Chirality : 0.053 0.129 870 Planarity : 0.002 0.015 830 Dihedral : 5.913 19.855 720 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.19 % Allowed : 15.53 % Favored : 81.28 % 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: -4.75 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.002 0.001 PHE A 94 TYR 0.003 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.579 Fit side-chains REVERT: A 72 THR cc_start: 0.9344 (m) cc_final: 0.9070 (m) REVERT: B 83 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7301 (mp0) REVERT: D 58 LYS cc_start: 0.7489 (ttmp) cc_final: 0.6856 (tptt) REVERT: E 58 LYS cc_start: 0.7494 (ttmp) cc_final: 0.7153 (tptt) REVERT: F 83 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7301 (mt-10) REVERT: H 83 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7053 (mp0) REVERT: I 58 LYS cc_start: 0.7660 (tttp) cc_final: 0.6819 (tptt) REVERT: I 83 GLU cc_start: 0.7869 (mp0) cc_final: 0.7502 (mp0) REVERT: J 58 LYS cc_start: 0.7821 (tttp) cc_final: 0.7238 (tptt) REVERT: J 83 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7419 (mp0) outliers start: 15 outliers final: 15 residues processed: 42 average time/residue: 0.1711 time to fit residues: 10.0602 Evaluate side-chains 45 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4910 Z= 0.331 Angle : 0.584 5.044 6630 Z= 0.340 Chirality : 0.054 0.132 870 Planarity : 0.002 0.014 830 Dihedral : 6.029 20.487 720 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 3.19 % Allowed : 16.60 % Favored : 80.21 % 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: -4.83 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.003 0.001 PHE A 94 TYR 0.010 0.002 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.478 Fit side-chains REVERT: A 72 THR cc_start: 0.9407 (m) cc_final: 0.9129 (m) REVERT: B 83 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7280 (mp0) REVERT: D 58 LYS cc_start: 0.7510 (ttmp) cc_final: 0.6865 (tptt) REVERT: E 58 LYS cc_start: 0.7518 (ttmp) cc_final: 0.7156 (tptt) REVERT: F 83 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7169 (mt-10) REVERT: G 83 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7468 (mp0) REVERT: I 58 LYS cc_start: 0.7657 (tttp) cc_final: 0.6795 (tptt) REVERT: J 58 LYS cc_start: 0.7830 (tttp) cc_final: 0.7244 (tptt) REVERT: J 83 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7426 (mp0) outliers start: 15 outliers final: 15 residues processed: 44 average time/residue: 0.1642 time to fit residues: 9.7838 Evaluate side-chains 51 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4195 r_free = 0.4195 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.107265 restraints weight = 6203.135| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.04 r_work: 0.3820 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4910 Z= 0.230 Angle : 0.562 5.411 6630 Z= 0.325 Chirality : 0.053 0.129 870 Planarity : 0.002 0.016 830 Dihedral : 5.930 20.226 720 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.19 % Allowed : 16.38 % Favored : 80.43 % 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: -4.74 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.002 0.001 PHE A 94 TYR 0.006 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.84 seconds wall clock time: 24 minutes 44.51 seconds (1484.51 seconds total)