Starting phenix.real_space_refine on Fri Aug 22 15:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rrr_19462/08_2025/8rrr_19462.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rrr_19462/08_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_19462/08_2025/8rrr_19462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rrr_19462/08_2025/8rrr_19462.map" model { file = "/net/cci-nas-00/data/ceres_data/8rrr_19462/08_2025/8rrr_19462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rrr_19462/08_2025/8rrr_19462.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.10, per 1000 atoms: 0.22 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: 0.37 Conformation dependent library (CDL) restraints added in 253.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 0.68 Time building geometry restraints manager: 0.51 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: 2.030 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.600 ------------------------------------------------------------------------------- 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= 0.294 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (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 TYR 0.020 0.004 TYR G 39 PHE 0.011 0.002 PHE A 94 HIS 0.004 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 4935) covalent geometry : angle 0.83307 ( 6665) hydrogen bonds : bond 0.14634 ( 94) hydrogen bonds : angle 7.66828 ( 306) *********************** 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 : 0.163 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: 0.0535 time to fit residues: 4.8078 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 : 0.171 ------------------------------------------------------------------------------- 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 49 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0050 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4459 r_free = 0.4459 target = 0.143566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.125540 restraints weight = 6875.814| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.97 r_work: 0.4160 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4935 Z= 0.123 Angle : 0.596 7.470 6665 Z= 0.334 Chirality : 0.053 0.121 875 Planarity : 0.002 0.010 835 Dihedral : 6.340 33.829 729 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.85 % Allowed : 17.45 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 39 PHE 0.010 0.001 PHE A 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4935) covalent geometry : angle 0.59605 ( 6665) hydrogen bonds : bond 0.01536 ( 94) hydrogen bonds : angle 4.27493 ( 306) *********************** 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 65 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.197 Fit side-chains REVERT: B 61 GLU cc_start: 0.8480 (mp0) cc_final: 0.8236 (mp0) REVERT: B 83 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: C 24 GLN cc_start: 0.6570 (mm110) cc_final: 0.5600 (pm20) REVERT: C 57 GLU cc_start: 0.7790 (tm-30) cc_final: 0.6584 (pm20) REVERT: D 24 GLN cc_start: 0.6523 (mp10) cc_final: 0.6262 (mp10) REVERT: D 57 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7651 (tt0) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.0515 time to fit residues: 4.7495 Evaluate side-chains 56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 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 55 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4351 r_free = 0.4351 target = 0.139171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.123101 restraints weight = 7222.326| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.70 r_work: 0.4069 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.053 4935 Z= 0.474 Angle : 0.882 6.489 6665 Z= 0.504 Chirality : 0.061 0.142 875 Planarity : 0.003 0.012 835 Dihedral : 7.632 30.807 725 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.62 % Allowed : 15.53 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.48 (0.24), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.18), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.006 TYR C 39 PHE 0.009 0.002 PHE A 94 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.01019 ( 4935) covalent geometry : angle 0.88193 ( 6665) hydrogen bonds : bond 0.02415 ( 94) hydrogen bonds : angle 4.80831 ( 306) *********************** 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 72 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.216 Fit side-chains REVERT: A 57 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 46 GLU cc_start: 0.8346 (tt0) cc_final: 0.8139 (tt0) REVERT: B 57 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7803 (tt0) REVERT: B 83 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: C 57 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: D 57 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7608 (tt0) REVERT: D 83 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: E 80 LYS cc_start: 0.7973 (mttt) cc_final: 0.7513 (mtmm) REVERT: F 80 LYS cc_start: 0.7623 (mtmt) cc_final: 0.6650 (mttm) REVERT: F 83 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6529 (mp0) outliers start: 17 outliers final: 9 residues processed: 64 average time/residue: 0.0541 time to fit residues: 4.8740 Evaluate side-chains 67 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 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 J residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.147724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.131734 restraints weight = 6876.407| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.57 r_work: 0.4186 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4935 Z= 0.143 Angle : 0.612 7.112 6665 Z= 0.344 Chirality : 0.053 0.124 875 Planarity : 0.002 0.010 835 Dihedral : 6.244 25.900 725 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.06 % Allowed : 18.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.15 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 PHE 0.009 0.001 PHE G 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4935) covalent geometry : angle 0.61219 ( 6665) hydrogen bonds : bond 0.01302 ( 94) hydrogen bonds : angle 3.84392 ( 306) *********************** 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 66 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.109 Fit side-chains REVERT: B 61 GLU cc_start: 0.8600 (mp0) cc_final: 0.8126 (mp0) REVERT: B 80 LYS cc_start: 0.7824 (mttp) cc_final: 0.7040 (mtmt) REVERT: B 83 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: C 57 GLU cc_start: 0.7719 (tm-30) cc_final: 0.6489 (pm20) REVERT: D 57 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7545 (tt0) REVERT: G 61 GLU cc_start: 0.8418 (mp0) cc_final: 0.7721 (mp0) outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.0409 time to fit residues: 3.8835 Evaluate side-chains 56 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 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 42 optimal weight: 20.0000 chunk 29 optimal weight: 0.0020 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.151300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.134752 restraints weight = 6777.020| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.63 r_work: 0.4218 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4935 Z= 0.153 Angle : 0.605 6.799 6665 Z= 0.340 Chirality : 0.053 0.124 875 Planarity : 0.002 0.010 835 Dihedral : 6.087 25.743 725 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.55 % Allowed : 18.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR F 39 PHE 0.008 0.001 PHE A 94 HIS 0.002 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4935) covalent geometry : angle 0.60476 ( 6665) hydrogen bonds : bond 0.01213 ( 94) hydrogen bonds : angle 3.67296 ( 306) *********************** 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: 12 poor density : 59 time to evaluate : 0.165 Fit side-chains REVERT: B 61 GLU cc_start: 0.8577 (mp0) cc_final: 0.8066 (mp0) REVERT: B 80 LYS cc_start: 0.7800 (mttp) cc_final: 0.6928 (mttp) REVERT: B 83 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: C 57 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6442 (pm20) REVERT: D 24 GLN cc_start: 0.6602 (mp10) cc_final: 0.6373 (mp10) REVERT: D 57 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7570 (tt0) REVERT: F 24 GLN cc_start: 0.6756 (mp10) cc_final: 0.6524 (mp10) REVERT: F 83 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: G 61 GLU cc_start: 0.8358 (mp0) cc_final: 0.7652 (mp0) REVERT: I 83 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6594 (mp0) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.0520 time to fit residues: 4.6825 Evaluate side-chains 64 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 C residue 92 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 83 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.142992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.126467 restraints weight = 7237.103| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.74 r_work: 0.4109 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 4935 Z= 0.332 Angle : 0.742 6.741 6665 Z= 0.421 Chirality : 0.057 0.126 875 Planarity : 0.002 0.011 835 Dihedral : 6.895 28.803 725 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.40 % Allowed : 17.87 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (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 TYR 0.018 0.004 TYR F 39 PHE 0.007 0.001 PHE A 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 4935) covalent geometry : angle 0.74162 ( 6665) hydrogen bonds : bond 0.01635 ( 94) hydrogen bonds : angle 4.13987 ( 306) *********************** 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 68 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.201 Fit side-chains REVERT: B 61 GLU cc_start: 0.8603 (mp0) cc_final: 0.8050 (mp0) REVERT: B 80 LYS cc_start: 0.7852 (mttp) cc_final: 0.6973 (mttp) REVERT: B 83 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: C 57 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: D 24 GLN cc_start: 0.6482 (mp10) cc_final: 0.6264 (mp10) REVERT: D 57 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7651 (tt0) REVERT: D 83 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: E 57 GLU cc_start: 0.7543 (tt0) cc_final: 0.7134 (tm-30) REVERT: E 80 LYS cc_start: 0.7985 (mttt) cc_final: 0.7558 (mttm) REVERT: F 61 GLU cc_start: 0.8506 (mp0) cc_final: 0.8238 (mp0) REVERT: F 80 LYS cc_start: 0.7667 (mtmt) cc_final: 0.6875 (mttp) REVERT: F 83 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: I 83 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6603 (mp0) outliers start: 16 outliers final: 9 residues processed: 59 average time/residue: 0.0661 time to fit residues: 5.3490 Evaluate side-chains 64 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 38 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 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 = 0.4444 r_free = 0.4444 target = 0.146794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.130386 restraints weight = 6971.092| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.68 r_work: 0.4167 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4935 Z= 0.226 Angle : 0.662 6.948 6665 Z= 0.374 Chirality : 0.054 0.124 875 Planarity : 0.002 0.010 835 Dihedral : 6.544 27.589 725 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.18 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR F 39 PHE 0.008 0.001 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 4935) covalent geometry : angle 0.66193 ( 6665) hydrogen bonds : bond 0.01369 ( 94) hydrogen bonds : angle 3.90708 ( 306) *********************** 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 75 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.239 Fit side-chains REVERT: B 61 GLU cc_start: 0.8604 (mp0) cc_final: 0.8027 (mp0) REVERT: B 80 LYS cc_start: 0.7864 (mttp) cc_final: 0.6978 (mttp) REVERT: B 83 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: C 57 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.6528 (pm20) REVERT: D 24 GLN cc_start: 0.6630 (mp10) cc_final: 0.6401 (mp10) REVERT: D 57 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7660 (tt0) REVERT: D 83 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: E 61 GLU cc_start: 0.8468 (mp0) cc_final: 0.8198 (mp0) REVERT: F 61 GLU cc_start: 0.8638 (mp0) cc_final: 0.8408 (mp0) REVERT: F 80 LYS cc_start: 0.7724 (mtmt) cc_final: 0.6850 (mttp) REVERT: F 83 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: I 83 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: J 83 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7026 (mp0) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.0563 time to fit residues: 5.3195 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 : 0.189 ------------------------------------------------------------------------------- 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 74 VAL 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 38 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 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 = 0.4435 r_free = 0.4435 target = 0.145961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.129520 restraints weight = 7101.769| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.69 r_work: 0.4152 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4935 Z= 0.244 Angle : 0.680 6.764 6665 Z= 0.384 Chirality : 0.055 0.124 875 Planarity : 0.002 0.014 835 Dihedral : 6.592 27.718 725 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.04 % Allowed : 16.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR F 39 PHE 0.008 0.001 PHE A 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 4935) covalent geometry : angle 0.68007 ( 6665) hydrogen bonds : bond 0.01391 ( 94) hydrogen bonds : angle 3.94677 ( 306) *********************** 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 74 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.187 Fit side-chains REVERT: B 61 GLU cc_start: 0.8611 (mp0) cc_final: 0.7907 (mp0) REVERT: B 80 LYS cc_start: 0.7928 (mttp) cc_final: 0.7051 (mttp) REVERT: B 83 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: C 57 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: D 24 GLN cc_start: 0.6709 (mp10) cc_final: 0.6492 (mp10) REVERT: D 57 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7697 (tt0) REVERT: D 83 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: E 83 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: F 24 GLN cc_start: 0.6986 (mp10) cc_final: 0.6751 (mp10) REVERT: F 61 GLU cc_start: 0.8637 (mp0) cc_final: 0.8295 (mp0) REVERT: F 80 LYS cc_start: 0.7807 (mtmt) cc_final: 0.6923 (mttp) REVERT: F 83 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: I 83 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: J 61 GLU cc_start: 0.8421 (mp0) cc_final: 0.8132 (mp0) REVERT: J 83 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7048 (mp0) outliers start: 19 outliers final: 12 residues processed: 66 average time/residue: 0.0508 time to fit residues: 4.7099 Evaluate side-chains 73 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 74 VAL 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 38 LEU 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 G residue 57 GLU 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 65 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- 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 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 = 0.4418 r_free = 0.4418 target = 0.144794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.128507 restraints weight = 7020.729| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.67 r_work: 0.4139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4935 Z= 0.265 Angle : 0.697 6.863 6665 Z= 0.393 Chirality : 0.055 0.125 875 Planarity : 0.002 0.012 835 Dihedral : 6.699 28.540 725 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.04 % Allowed : 16.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR F 39 PHE 0.008 0.001 PHE A 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 4935) covalent geometry : angle 0.69703 ( 6665) hydrogen bonds : bond 0.01438 ( 94) hydrogen bonds : angle 4.01946 ( 306) *********************** 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 74 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.236 Fit side-chains REVERT: B 80 LYS cc_start: 0.7881 (mttp) cc_final: 0.7096 (mttp) REVERT: B 83 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: C 57 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6582 (pm20) REVERT: D 24 GLN cc_start: 0.6632 (mp10) cc_final: 0.6393 (mp10) REVERT: D 57 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7653 (tt0) REVERT: D 83 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: E 83 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: F 24 GLN cc_start: 0.6958 (mp10) cc_final: 0.6654 (mp10) REVERT: F 61 GLU cc_start: 0.8611 (mp0) cc_final: 0.8212 (mp0) REVERT: F 80 LYS cc_start: 0.7758 (mtmt) cc_final: 0.6880 (mttp) REVERT: F 83 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: I 83 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: J 83 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7090 (mp0) outliers start: 19 outliers final: 12 residues processed: 66 average time/residue: 0.0604 time to fit residues: 5.5930 Evaluate side-chains 73 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 74 VAL 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 38 LEU 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 G residue 57 GLU 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 58 optimal weight: 7.9990 chunk 63 optimal weight: 0.0670 chunk 62 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- 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 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 = 0.4479 r_free = 0.4479 target = 0.149546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.132917 restraints weight = 6868.626| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.71 r_work: 0.4199 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4935 Z= 0.165 Angle : 0.623 6.831 6665 Z= 0.349 Chirality : 0.053 0.125 875 Planarity : 0.002 0.022 835 Dihedral : 6.180 25.992 725 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.83 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.07 (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 TYR 0.013 0.002 TYR F 39 PHE 0.008 0.001 PHE A 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4935) covalent geometry : angle 0.62301 ( 6665) hydrogen bonds : bond 0.01192 ( 94) hydrogen bonds : angle 3.70278 ( 306) ********************** 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 79 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.196 Fit side-chains REVERT: B 80 LYS cc_start: 0.7820 (mttp) cc_final: 0.6930 (mttp) REVERT: B 83 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: C 57 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6545 (pm20) REVERT: D 24 GLN cc_start: 0.6758 (mp10) cc_final: 0.6550 (mp10) REVERT: D 57 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7638 (tt0) REVERT: D 83 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: E 83 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: F 24 GLN cc_start: 0.6812 (mp10) cc_final: 0.6556 (mp10) REVERT: F 61 GLU cc_start: 0.8643 (mp0) cc_final: 0.8315 (mp0) REVERT: F 80 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7061 (mtmt) REVERT: F 83 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: H 20 GLU cc_start: 0.7283 (mp0) cc_final: 0.7059 (mp0) REVERT: I 83 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: J 83 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7031 (mp0) outliers start: 18 outliers final: 11 residues processed: 71 average time/residue: 0.0588 time to fit residues: 5.7973 Evaluate side-chains 76 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 74 VAL 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 38 LEU Chi-restraints excluded: chain E residue 83 GLU 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 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 38 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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 = 0.4423 r_free = 0.4423 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.128651 restraints weight = 7049.440| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.69 r_work: 0.4137 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4935 Z= 0.263 Angle : 0.705 6.624 6665 Z= 0.395 Chirality : 0.055 0.127 875 Planarity : 0.003 0.027 835 Dihedral : 6.605 28.597 725 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.83 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.14 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYR C 39 PHE 0.007 0.001 PHE A 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 4935) covalent geometry : angle 0.70454 ( 6665) hydrogen bonds : bond 0.01381 ( 94) hydrogen bonds : angle 3.95728 ( 306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 933.01 seconds wall clock time: 16 minutes 52.28 seconds (1012.28 seconds total)