Starting phenix.real_space_refine on Tue Jan 14 01:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.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/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.map" model { file = "/net/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rrr_19462/01_2025/8rrr_19462.cif" } 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= 0.001 sd= 0.003 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 3065 2.51 5 N 865 2.21 5 O 995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4925 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 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: 4.00, per 1000 atoms: 0.81 Number of scatterers: 4925 At special positions: 0 Unit cell: (82.95, 113.4, 42, 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 995 8.00 N 865 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 688.6 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.104A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 20 removed outlier: 8.728A pdb=" N GLU D 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.074A pdb=" N LEU A 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY D 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.383A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY A 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS D 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.893A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.982A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.903A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.386A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR A 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA D 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.323A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA D 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR D 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER D 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ALA E 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.251A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.177A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY I 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.362A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N HIS J 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 55 removed outlier: 6.077A pdb=" N THR F 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 61 through 66 removed outlier: 6.754A pdb=" N GLU F 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR H 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL H 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 69 through 71 removed outlier: 7.054A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 75 through 79 removed outlier: 6.544A pdb=" N ALA F 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN H 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 93 removed outlier: 6.421A pdb=" N SER F 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA G 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA F 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR G 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA F 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA I 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR I 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA G 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR J 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA I 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 306 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: 1.30 Time building geometry restraints manager: 1.44 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: 875 1.28 - 1.35: 775 1.35 - 1.42: 180 1.42 - 1.48: 835 1.48 - 1.55: 2270 Bond restraints: 4935 Sorted by residual: bond pdb=" CA GLY D 93 " pdb=" C GLY D 93 " ideal model delta sigma weight residual 1.530 1.512 0.019 1.04e-02 9.25e+03 3.23e+00 bond pdb=" C ALA I 85 " pdb=" N GLY I 86 " ideal model delta sigma weight residual 1.331 1.319 0.012 6.60e-03 2.30e+04 3.19e+00 bond pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 1.464 1.446 0.018 1.12e-02 7.97e+03 2.59e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" C THR J 59 " pdb=" N LYS J 60 " ideal model delta sigma weight residual 1.333 1.311 0.021 1.45e-02 4.76e+03 2.14e+00 ... (remaining 4930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6263 1.49 - 2.98: 334 2.98 - 4.47: 35 4.47 - 5.96: 21 5.96 - 7.45: 12 Bond angle restraints: 6665 Sorted by residual: angle pdb=" C GLU J 83 " pdb=" CA GLU J 83 " pdb=" CB GLU J 83 " ideal model delta sigma weight residual 111.45 105.31 6.14 1.72e+00 3.38e-01 1.27e+01 angle pdb=" C GLU H 83 " pdb=" CA GLU H 83 " pdb=" CB GLU H 83 " ideal model delta sigma weight residual 111.45 105.63 5.82 1.72e+00 3.38e-01 1.14e+01 angle pdb=" C GLU C 83 " pdb=" N GLY C 84 " pdb=" CA GLY C 84 " ideal model delta sigma weight residual 121.41 114.90 6.51 1.96e+00 2.60e-01 1.10e+01 angle pdb=" C GLU C 83 " pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 111.28 106.21 5.07 1.58e+00 4.01e-01 1.03e+01 angle pdb=" C GLU E 83 " pdb=" N GLY E 84 " pdb=" CA GLY E 84 " ideal model delta sigma weight residual 121.41 115.19 6.22 1.96e+00 2.60e-01 1.01e+01 ... (remaining 6660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2506 15.89 - 31.78: 265 31.78 - 47.67: 62 47.67 - 63.56: 17 63.56 - 79.45: 5 Dihedral angle restraints: 2855 sinusoidal: 900 harmonic: 1955 Sorted by residual: dihedral pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " pdb=" CA ALA A 85 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+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 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 442 0.033 - 0.066: 237 0.066 - 0.099: 92 0.099 - 0.131: 101 0.131 - 0.164: 3 Chirality restraints: 875 Sorted by residual: chirality pdb=" CG LEU C 38 " pdb=" CB LEU C 38 " pdb=" CD1 LEU C 38 " pdb=" CD2 LEU C 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CG LEU G 38 " pdb=" CB LEU G 38 " pdb=" CD1 LEU G 38 " pdb=" CD2 LEU G 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 872 not shown) Planarity restraints: 835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 61 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" CD GLU E 61 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU E 61 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 61 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 61 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" CD GLU J 61 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU J 61 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU J 61 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 61 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" CD GLU F 61 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU F 61 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU F 61 " 0.009 2.00e-02 2.50e+03 ... (remaining 832 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1622 2.83 - 3.35: 4131 3.35 - 3.87: 8146 3.87 - 4.38: 8663 4.38 - 4.90: 17468 Nonbonded interactions: 40030 Sorted by model distance: nonbonded pdb=" O THR B 72 " pdb=" OG1 THR B 72 " model vdw 2.315 3.040 nonbonded pdb=" N GLN F 24 " pdb=" OE1 GLN F 24 " model vdw 2.341 3.120 nonbonded pdb=" O THR H 72 " pdb=" OG1 THR H 72 " model vdw 2.342 3.040 nonbonded pdb=" NZ LYS I 45 " pdb=" OE1 GLU I 46 " model vdw 2.359 3.120 nonbonded pdb=" N GLN A 24 " pdb=" OE1 GLN A 24 " model vdw 2.369 3.120 ... (remaining 40025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 96) selection = (chain 'B' and resid 14 through 96) selection = (chain 'C' and resid 14 through 96) selection = (chain 'D' and resid 14 through 96) selection = (chain 'E' and resid 14 through 96) 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.410 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.006 0.051 4935 Z= 0.400 Angle : 0.833 7.448 6665 Z= 0.486 Chirality : 0.055 0.164 875 Planarity : 0.002 0.016 835 Dihedral : 15.099 79.447 1625 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.64 % Allowed : 17.23 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 PHE 0.011 0.002 PHE A 94 TYR 0.020 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.538 Fit side-chains REVERT: C 24 GLN cc_start: 0.7034 (mm110) cc_final: 0.6114 (pm20) REVERT: C 57 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: D 57 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7491 (tt0) REVERT: E 80 LYS cc_start: 0.8114 (mttt) cc_final: 0.7696 (mttm) REVERT: F 80 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7714 (mttp) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1493 time to fit residues: 13.2081 Evaluate side-chains 59 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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** H 24 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.138411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.120472 restraints weight = 7039.588| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.96 r_work: 0.4074 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4935 Z= 0.280 Angle : 0.647 7.293 6665 Z= 0.364 Chirality : 0.053 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 6.794 33.123 729 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.70 % Allowed : 15.32 % Favored : 82.98 % 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: -4.17 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.547 Fit side-chains REVERT: B 61 GLU cc_start: 0.8447 (mp0) cc_final: 0.8072 (mp0) REVERT: B 83 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: C 24 GLN cc_start: 0.6624 (mm110) cc_final: 0.5850 (pm20) REVERT: C 57 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6564 (pm20) REVERT: D 57 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7679 (tt0) REVERT: F 80 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7150 (mttm) REVERT: I 24 GLN cc_start: 0.7395 (mp10) cc_final: 0.7053 (mp10) outliers start: 8 outliers final: 2 residues processed: 62 average time/residue: 0.1307 time to fit residues: 11.4187 Evaluate side-chains 55 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 52 optimal weight: 0.0570 overall best weight: 4.8106 ------------------------------------------------------------------------------- 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** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.142327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.126384 restraints weight = 7057.135| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.53 r_work: 0.4120 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4935 Z= 0.395 Angle : 0.696 6.914 6665 Z= 0.394 Chirality : 0.055 0.125 875 Planarity : 0.002 0.010 835 Dihedral : 7.100 40.653 728 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.40 % Allowed : 16.17 % 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: -4.21 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.019 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.504 Fit side-chains REVERT: B 83 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: C 57 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: D 57 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7748 (tt0) REVERT: F 61 GLU cc_start: 0.8697 (mp0) cc_final: 0.8492 (mp0) REVERT: F 80 LYS cc_start: 0.7846 (mtmt) cc_final: 0.6672 (mttm) REVERT: F 83 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.6824 (mp0) outliers start: 16 outliers final: 9 residues processed: 65 average time/residue: 0.1393 time to fit residues: 12.5519 Evaluate side-chains 63 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.0040 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 overall best weight: 2.8198 ------------------------------------------------------------------------------- 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** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.146619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.130476 restraints weight = 7056.896| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.59 r_work: 0.4171 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4935 Z= 0.250 Angle : 0.617 6.911 6665 Z= 0.347 Chirality : 0.053 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 6.626 40.526 728 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.91 % Allowed : 17.45 % Favored : 80.64 % 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: -4.08 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.014 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.543 Fit side-chains REVERT: B 61 GLU cc_start: 0.8618 (mp0) cc_final: 0.8104 (mp0) REVERT: B 83 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: C 24 GLN cc_start: 0.6665 (mm110) cc_final: 0.5770 (pm20) REVERT: C 57 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: D 57 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7569 (tt0) REVERT: D 83 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: F 61 GLU cc_start: 0.8532 (mp0) cc_final: 0.8270 (mp0) REVERT: F 80 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7213 (mtmt) REVERT: F 83 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: J 24 GLN cc_start: 0.6610 (mp10) cc_final: 0.6178 (mp10) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.1387 time to fit residues: 12.9244 Evaluate side-chains 62 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** H 24 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 = 0.4439 r_free = 0.4439 target = 0.146109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.129657 restraints weight = 7028.118| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.70 r_work: 0.4161 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4935 Z= 0.380 Angle : 0.685 6.747 6665 Z= 0.387 Chirality : 0.055 0.125 875 Planarity : 0.002 0.010 835 Dihedral : 6.948 43.313 728 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.62 % Allowed : 16.38 % Favored : 80.00 % 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: -4.13 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.017 0.004 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.507 Fit side-chains REVERT: B 61 GLU cc_start: 0.8635 (mp0) cc_final: 0.8134 (mp0) REVERT: B 83 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: C 57 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: D 57 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7668 (tt0) REVERT: D 83 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: F 61 GLU cc_start: 0.8556 (mp0) cc_final: 0.8213 (mp0) REVERT: F 80 LYS cc_start: 0.7745 (mtmt) cc_final: 0.6540 (mttm) REVERT: F 83 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: I 83 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: J 24 GLN cc_start: 0.6587 (mp10) cc_final: 0.6065 (mp10) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.1320 time to fit residues: 11.8314 Evaluate side-chains 67 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 0.0050 chunk 7 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 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 = 0.4498 r_free = 0.4498 target = 0.150532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.133759 restraints weight = 6820.246| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.68 r_work: 0.4217 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4935 Z= 0.225 Angle : 0.611 6.881 6665 Z= 0.342 Chirality : 0.053 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 6.477 42.492 728 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.40 % Allowed : 17.23 % Favored : 79.36 % 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: -4.03 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 50 PHE 0.008 0.001 PHE A 94 TYR 0.012 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.592 Fit side-chains REVERT: B 61 GLU cc_start: 0.8608 (mp0) cc_final: 0.8068 (mp0) REVERT: B 83 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: C 57 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: D 57 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7541 (tt0) REVERT: D 83 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: F 61 GLU cc_start: 0.8533 (mp0) cc_final: 0.8314 (mp0) REVERT: F 80 LYS cc_start: 0.7591 (mtmt) cc_final: 0.6729 (mtmt) REVERT: F 83 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: I 83 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: J 24 GLN cc_start: 0.6752 (mp10) cc_final: 0.6171 (mp10) REVERT: J 61 GLU cc_start: 0.8380 (mp0) cc_final: 0.8058 (mp0) REVERT: J 83 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7057 (mp0) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1336 time to fit residues: 12.1861 Evaluate side-chains 68 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.126117 restraints weight = 7083.006| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.72 r_work: 0.4118 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.008 0.064 4935 Z= 0.520 Angle : 0.765 6.848 6665 Z= 0.432 Chirality : 0.057 0.138 875 Planarity : 0.003 0.014 835 Dihedral : 7.286 46.263 728 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.83 % Allowed : 17.23 % Favored : 78.94 % 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: -4.25 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.007 0.001 PHE A 94 TYR 0.021 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.520 Fit side-chains REVERT: B 61 GLU cc_start: 0.8602 (mp0) cc_final: 0.8023 (mp0) REVERT: B 83 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: C 57 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: D 57 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7552 (tt0) REVERT: D 83 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: E 80 LYS cc_start: 0.7957 (mttt) cc_final: 0.7532 (mttm) REVERT: F 61 GLU cc_start: 0.8478 (mp0) cc_final: 0.7929 (mp0) REVERT: F 80 LYS cc_start: 0.7610 (mtmt) cc_final: 0.6769 (mtmt) REVERT: F 83 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: I 83 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: J 83 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6959 (mp0) outliers start: 18 outliers final: 11 residues processed: 64 average time/residue: 0.1335 time to fit residues: 11.7940 Evaluate side-chains 65 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU 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 0 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 24 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 = 0.4456 r_free = 0.4456 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.131415 restraints weight = 6973.958| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.61 r_work: 0.4178 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4935 Z= 0.293 Angle : 0.649 6.857 6665 Z= 0.364 Chirality : 0.054 0.124 875 Planarity : 0.002 0.011 835 Dihedral : 6.794 47.076 728 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.47 % Allowed : 16.38 % Favored : 79.15 % 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: -4.13 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.515 Fit side-chains REVERT: B 61 GLU cc_start: 0.8591 (mp0) cc_final: 0.8006 (mp0) REVERT: B 83 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 57 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: D 57 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7655 (tt0) REVERT: D 83 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: E 83 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: F 24 GLN cc_start: 0.6756 (mp10) cc_final: 0.6469 (mp10) REVERT: F 61 GLU cc_start: 0.8538 (mp0) cc_final: 0.7945 (mp0) REVERT: F 80 LYS cc_start: 0.7785 (mtmt) cc_final: 0.6995 (mtmt) REVERT: F 83 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: I 83 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: J 61 GLU cc_start: 0.8401 (mp0) cc_final: 0.8105 (mp0) REVERT: J 83 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7011 (mp0) outliers start: 21 outliers final: 10 residues processed: 71 average time/residue: 0.1236 time to fit residues: 12.3579 Evaluate side-chains 68 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU 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 45 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 33 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 3.2102 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.148102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.131612 restraints weight = 6830.784| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.66 r_work: 0.4192 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4935 Z= 0.283 Angle : 0.644 6.794 6665 Z= 0.360 Chirality : 0.054 0.123 875 Planarity : 0.002 0.017 835 Dihedral : 6.683 46.649 728 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.62 % Allowed : 17.02 % Favored : 79.36 % 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: -4.07 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.531 Fit side-chains REVERT: B 61 GLU cc_start: 0.8582 (mp0) cc_final: 0.8065 (mp0) REVERT: B 83 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: C 57 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6594 (pm20) REVERT: D 57 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7655 (tt0) REVERT: D 83 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: E 83 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: F 24 GLN cc_start: 0.6819 (mp10) cc_final: 0.6603 (mp10) REVERT: F 61 GLU cc_start: 0.8588 (mp0) cc_final: 0.8023 (mp0) REVERT: F 80 LYS cc_start: 0.7760 (mtmt) cc_final: 0.6979 (mtmt) REVERT: F 83 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: I 83 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: J 61 GLU cc_start: 0.8448 (mp0) cc_final: 0.8050 (mp0) REVERT: J 83 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7070 (mp0) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.1269 time to fit residues: 12.0935 Evaluate side-chains 70 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU 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 29 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 24 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 = 0.4383 r_free = 0.4383 target = 0.141588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.125401 restraints weight = 7155.620| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.65 r_work: 0.4104 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 4935 Z= 0.535 Angle : 0.791 8.069 6665 Z= 0.445 Chirality : 0.058 0.169 875 Planarity : 0.003 0.022 835 Dihedral : 7.414 48.894 728 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 3.40 % Allowed : 17.66 % Favored : 78.94 % 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: -4.32 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.001 PHE F 94 TYR 0.023 0.004 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.218 Fit side-chains REVERT: B 61 GLU cc_start: 0.8598 (mp0) cc_final: 0.8331 (mp0) REVERT: B 83 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: C 57 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: D 57 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7642 (tt0) REVERT: D 83 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: E 80 LYS cc_start: 0.8050 (mttt) cc_final: 0.7659 (mttm) REVERT: E 83 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: F 24 GLN cc_start: 0.6808 (mp10) cc_final: 0.6603 (mp10) REVERT: F 61 GLU cc_start: 0.8485 (mp0) cc_final: 0.8100 (mp0) REVERT: F 80 LYS cc_start: 0.7798 (mtmt) cc_final: 0.6940 (mtmt) REVERT: F 83 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: I 83 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: J 83 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7094 (mp0) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.1400 time to fit residues: 12.0027 Evaluate side-chains 63 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU 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 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.154283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.137390 restraints weight = 6717.458| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.72 r_work: 0.4263 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4935 Z= 0.177 Angle : 0.606 6.992 6665 Z= 0.337 Chirality : 0.053 0.125 875 Planarity : 0.002 0.026 835 Dihedral : 6.290 47.966 728 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.98 % Allowed : 17.66 % Favored : 79.36 % 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: -4.03 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.008 0.001 PHE A 94 TYR 0.011 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.92 seconds wall clock time: 34 minutes 51.07 seconds (2091.07 seconds total)