Starting phenix.real_space_refine on Fri Dec 27 05:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615.map" model { file = "/net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wmm_32615/12_2024/7wmm_32615_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 2 5.16 5 C 1650 2.51 5 N 448 2.21 5 O 514 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "B" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "C" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "D" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "E" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "F" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER A 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 42 " occ=0.50 residue: pdb=" N ASER B 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 42 " occ=0.50 residue: pdb=" N ASER C 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 42 " occ=0.50 residue: pdb=" N ASER D 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 42 " occ=0.50 residue: pdb=" N ASER E 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 42 " occ=0.50 residue: pdb=" N ASER F 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER F 42 " occ=0.50 Time building chain proxies: 3.70, per 1000 atoms: 1.41 Number of scatterers: 2618 At special positions: 0 Unit cell: (98.77, 105.41, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 2 16.00 F 2 9.00 O 514 8.00 N 448 7.00 C 1650 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: 0.75 Conformation dependent library (CDL) restraints added in 712.6 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 70.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.746A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 41 " --> pdb=" O ASER B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 66 removed outlier: 6.966A pdb=" N GLU B 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY A 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU A 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 59 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLY E 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N HIS A 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ALA E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N VAL A 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.408A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N GLU E 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N THR E 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS A 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU E 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS A 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL E 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN A 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASN E 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 82 removed outlier: 6.898A pdb=" N VAL B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA B 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN A 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N GLY E 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR A 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N THR E 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N GLN E 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ALA A 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N THR E 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N LYS A 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 92 removed outlier: 8.966A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ALA B 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER A 87 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE E 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.685A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 41 " --> pdb=" O ASER D 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 45 through 66 removed outlier: 6.967A pdb=" N GLU D 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA D 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU C 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS D 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 59 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL F 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N THR F 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS C 58 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLU F 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS C 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL F 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN C 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN F 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.912A pdb=" N VAL D 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR D 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY C 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN C 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS D 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N VAL C 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N GLY F 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR C 72 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N THR F 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA C 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N GLN F 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N ALA C 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N THR F 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N LYS C 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 92 removed outlier: 8.927A pdb=" N GLY C 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N ALA D 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER C 87 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 88 " --> pdb=" O SER C 87 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.54 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 850 1.37 - 1.51: 864 1.51 - 1.66: 922 1.66 - 1.80: 2 1.80 - 1.94: 2 Bond restraints: 2640 Sorted by residual: bond pdb=" C16 1KI C 201 " pdb=" S27 1KI C 201 " ideal model delta sigma weight residual 1.770 1.668 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C18 1KI A 201 " pdb=" C19 1KI A 201 " ideal model delta sigma weight residual 1.454 1.555 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C16 1KI A 201 " pdb=" S27 1KI A 201 " ideal model delta sigma weight residual 1.770 1.669 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C18 1KI C 201 " pdb=" C19 1KI C 201 " ideal model delta sigma weight residual 1.454 1.554 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C16 1KI A 201 " pdb=" N15 1KI A 201 " ideal model delta sigma weight residual 1.303 1.396 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 3568 4.61 - 9.23: 10 9.23 - 13.84: 0 13.84 - 18.46: 0 18.46 - 23.07: 2 Bond angle restraints: 3580 Sorted by residual: angle pdb=" C17 1KI C 201 " pdb=" C18 1KI C 201 " pdb=" C19 1KI C 201 " ideal model delta sigma weight residual 126.82 103.75 23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C17 1KI A 201 " pdb=" C18 1KI A 201 " pdb=" C19 1KI A 201 " ideal model delta sigma weight residual 126.82 103.76 23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C13 1KI C 201 " pdb=" S27 1KI C 201 " pdb=" C16 1KI C 201 " ideal model delta sigma weight residual 89.32 98.45 -9.13 3.00e+00 1.11e-01 9.27e+00 angle pdb=" C13 1KI A 201 " pdb=" S27 1KI A 201 " pdb=" C16 1KI A 201 " ideal model delta sigma weight residual 89.32 98.44 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" C05 1KI A 201 " pdb=" N04 1KI A 201 " pdb=" C11 1KI A 201 " ideal model delta sigma weight residual 112.35 119.89 -7.54 3.00e+00 1.11e-01 6.32e+00 ... (remaining 3575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1449 16.30 - 32.60: 53 32.60 - 48.90: 17 48.90 - 65.20: 7 65.20 - 81.50: 6 Dihedral angle restraints: 1532 sinusoidal: 518 harmonic: 1014 Sorted by residual: dihedral pdb=" CB GLU D 46 " pdb=" CG GLU D 46 " pdb=" CD GLU D 46 " pdb=" OE1 GLU D 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.50 -81.50 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " pdb=" CD GLU C 46 " pdb=" OE1 GLU C 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.47 -81.47 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU F 46 " pdb=" CG GLU F 46 " pdb=" CD GLU F 46 " pdb=" OE1 GLU F 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.40 -81.40 1 3.00e+01 1.11e-03 9.07e+00 ... (remaining 1529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 158 0.025 - 0.049: 182 0.049 - 0.074: 41 0.074 - 0.099: 18 0.099 - 0.123: 63 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 459 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.005 2.00e-02 2.50e+03 5.43e-03 4.42e-01 pdb=" CG HIS A 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.005 2.00e-02 2.50e+03 5.32e-03 4.25e-01 pdb=" CG HIS B 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.005 2.00e-02 2.50e+03 5.15e-03 3.98e-01 pdb=" CG HIS E 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.002 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 810 2.87 - 3.38: 2137 3.38 - 3.88: 4309 3.88 - 4.39: 4351 4.39 - 4.90: 9013 Nonbonded interactions: 20620 Sorted by model distance: nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS E 80 " model vdw 2.361 3.120 nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU B 46 " model vdw 2.366 3.120 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS F 80 " model vdw 2.377 3.120 nonbonded pdb=" NZ LYS C 80 " pdb=" OE1 GLU D 46 " model vdw 2.378 3.120 nonbonded pdb=" OE1 GLU A 83 " pdb=" F10 1KI A 201 " model vdw 2.458 2.990 ... (remaining 20615 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 37 through 41 or resid 43 through 97)) selection = (chain 'B' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'C' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'D' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'E' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'F' and (resid 37 through 41 or resid 43 through 97)) } 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=0.50 max=1.00 mean=0.99 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.460 Find NCS groups from input model: 0.140 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 : 0.008 0.102 2640 Z= 0.476 Angle : 0.859 23.070 3580 Z= 0.370 Chirality : 0.053 0.123 462 Planarity : 0.002 0.005 440 Dihedral : 12.788 81.499 896 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.006 0.002 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.290 Fit side-chains REVERT: A 94 PHE cc_start: 0.7566 (p90) cc_final: 0.7054 (p90) REVERT: B 46 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 38 LEU cc_start: 0.8809 (tp) cc_final: 0.8583 (tm) REVERT: C 46 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 94 PHE cc_start: 0.7546 (p90) cc_final: 0.6798 (p90) REVERT: D 94 PHE cc_start: 0.7724 (p90) cc_final: 0.7503 (p90) REVERT: E 38 LEU cc_start: 0.8894 (tp) cc_final: 0.8670 (tm) REVERT: E 94 PHE cc_start: 0.7910 (p90) cc_final: 0.7489 (p90) REVERT: F 94 PHE cc_start: 0.7880 (p90) cc_final: 0.7603 (p90) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.4697 time to fit residues: 107.8221 Evaluate side-chains 59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2640 Z= 0.422 Angle : 0.877 13.177 3580 Z= 0.421 Chirality : 0.060 0.143 462 Planarity : 0.003 0.020 440 Dihedral : 6.656 51.828 398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.14 % Allowed : 13.26 % Favored : 85.61 % 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: -2.69 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS A 50 PHE 0.009 0.002 PHE F 94 TYR 0.007 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.285 Fit side-chains REVERT: A 94 PHE cc_start: 0.7593 (p90) cc_final: 0.7068 (p90) REVERT: B 46 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 46 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 94 PHE cc_start: 0.7605 (p90) cc_final: 0.6923 (p90) REVERT: D 94 PHE cc_start: 0.7686 (p90) cc_final: 0.7483 (p90) REVERT: E 38 LEU cc_start: 0.8885 (tp) cc_final: 0.8631 (tm) REVERT: E 94 PHE cc_start: 0.7899 (p90) cc_final: 0.7510 (p90) REVERT: F 44 THR cc_start: 0.8661 (m) cc_final: 0.8088 (p) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 1.2215 time to fit residues: 79.9607 Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2640 Z= 0.147 Angle : 0.695 10.546 3580 Z= 0.315 Chirality : 0.053 0.124 462 Planarity : 0.002 0.014 440 Dihedral : 5.153 40.767 398 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.14 % Allowed : 16.67 % Favored : 82.20 % 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: -2.34 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.008 0.002 PHE B 94 TYR 0.006 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.292 Fit side-chains REVERT: A 94 PHE cc_start: 0.7637 (p90) cc_final: 0.7156 (p90) REVERT: B 46 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 94 PHE cc_start: 0.7528 (p90) cc_final: 0.7307 (p90) REVERT: C 94 PHE cc_start: 0.7573 (p90) cc_final: 0.6891 (p90) REVERT: D 44 THR cc_start: 0.8320 (m) cc_final: 0.7996 (p) REVERT: D 94 PHE cc_start: 0.7600 (p90) cc_final: 0.7164 (p90) REVERT: E 38 LEU cc_start: 0.8863 (tp) cc_final: 0.8648 (tm) REVERT: E 44 THR cc_start: 0.8511 (m) cc_final: 0.8138 (p) REVERT: E 94 PHE cc_start: 0.7879 (p90) cc_final: 0.7517 (p90) REVERT: F 44 THR cc_start: 0.8672 (m) cc_final: 0.8241 (p) outliers start: 3 outliers final: 0 residues processed: 61 average time/residue: 1.0319 time to fit residues: 64.6907 Evaluate side-chains 60 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2640 Z= 0.158 Angle : 0.675 10.058 3580 Z= 0.308 Chirality : 0.053 0.127 462 Planarity : 0.002 0.013 440 Dihedral : 5.046 41.162 398 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.14 % Allowed : 17.05 % Favored : 81.82 % 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: -2.22 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.006 0.002 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.288 Fit side-chains REVERT: A 94 PHE cc_start: 0.7590 (p90) cc_final: 0.7123 (p90) REVERT: B 46 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 94 PHE cc_start: 0.7482 (p90) cc_final: 0.7217 (p90) REVERT: C 94 PHE cc_start: 0.7583 (p90) cc_final: 0.6917 (p90) REVERT: D 44 THR cc_start: 0.8340 (m) cc_final: 0.8033 (p) REVERT: D 94 PHE cc_start: 0.7616 (p90) cc_final: 0.7138 (p90) REVERT: E 38 LEU cc_start: 0.8911 (tp) cc_final: 0.8668 (tm) REVERT: E 44 THR cc_start: 0.8523 (m) cc_final: 0.8128 (p) REVERT: E 94 PHE cc_start: 0.7855 (p90) cc_final: 0.7516 (p90) REVERT: F 44 THR cc_start: 0.8635 (m) cc_final: 0.8171 (p) outliers start: 3 outliers final: 1 residues processed: 60 average time/residue: 0.9676 time to fit residues: 59.7744 Evaluate side-chains 61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2640 Z= 0.334 Angle : 0.811 12.398 3580 Z= 0.379 Chirality : 0.057 0.136 462 Planarity : 0.002 0.011 440 Dihedral : 5.566 40.619 398 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.89 % Allowed : 16.29 % Favored : 81.82 % 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: -2.39 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.008 0.002 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.306 Fit side-chains REVERT: A 94 PHE cc_start: 0.7651 (p90) cc_final: 0.7160 (p90) REVERT: B 46 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 94 PHE cc_start: 0.7586 (p90) cc_final: 0.6947 (p90) REVERT: D 44 THR cc_start: 0.8490 (m) cc_final: 0.8114 (p) REVERT: D 94 PHE cc_start: 0.7670 (p90) cc_final: 0.7196 (p90) REVERT: E 38 LEU cc_start: 0.8870 (tp) cc_final: 0.8634 (tm) REVERT: F 44 THR cc_start: 0.8582 (m) cc_final: 0.8034 (p) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 1.1941 time to fit residues: 72.1992 Evaluate side-chains 57 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2640 Z= 0.298 Angle : 0.796 12.103 3580 Z= 0.370 Chirality : 0.056 0.135 462 Planarity : 0.002 0.011 440 Dihedral : 5.459 41.693 398 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.89 % Allowed : 16.67 % Favored : 81.44 % 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: -2.38 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.010 0.002 PHE E 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.291 Fit side-chains REVERT: A 94 PHE cc_start: 0.7634 (p90) cc_final: 0.7143 (p90) REVERT: B 46 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 94 PHE cc_start: 0.7556 (p90) cc_final: 0.6907 (p90) REVERT: D 44 THR cc_start: 0.8473 (m) cc_final: 0.8094 (p) REVERT: D 94 PHE cc_start: 0.7660 (p90) cc_final: 0.7184 (p90) REVERT: E 38 LEU cc_start: 0.8902 (tp) cc_final: 0.8660 (tm) REVERT: E 44 THR cc_start: 0.8386 (m) cc_final: 0.7925 (p) REVERT: F 44 THR cc_start: 0.8567 (m) cc_final: 0.8044 (p) outliers start: 5 outliers final: 0 residues processed: 60 average time/residue: 1.1122 time to fit residues: 68.4594 Evaluate side-chains 59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2640 Z= 0.178 Angle : 0.709 10.765 3580 Z= 0.324 Chirality : 0.053 0.126 462 Planarity : 0.002 0.013 440 Dihedral : 5.149 44.396 398 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.38 % Allowed : 18.56 % Favored : 81.06 % 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: -2.20 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.011 0.002 PHE E 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.308 Fit side-chains REVERT: A 94 PHE cc_start: 0.7598 (p90) cc_final: 0.7121 (p90) REVERT: B 94 PHE cc_start: 0.7523 (p90) cc_final: 0.7300 (p90) REVERT: C 94 PHE cc_start: 0.7536 (p90) cc_final: 0.6919 (p90) REVERT: D 44 THR cc_start: 0.8437 (m) cc_final: 0.8058 (p) REVERT: D 94 PHE cc_start: 0.7641 (p90) cc_final: 0.7179 (p90) REVERT: E 38 LEU cc_start: 0.8862 (tp) cc_final: 0.8646 (tm) REVERT: E 44 THR cc_start: 0.8477 (m) cc_final: 0.8092 (p) REVERT: F 44 THR cc_start: 0.8578 (m) cc_final: 0.8106 (p) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 1.1037 time to fit residues: 70.2295 Evaluate side-chains 58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2640 Z= 0.139 Angle : 0.662 9.507 3580 Z= 0.301 Chirality : 0.053 0.125 462 Planarity : 0.002 0.012 440 Dihedral : 4.907 43.501 398 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.38 % Allowed : 18.56 % Favored : 81.06 % 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: -2.05 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.010 0.002 PHE E 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.299 Fit side-chains REVERT: A 94 PHE cc_start: 0.7588 (p90) cc_final: 0.7132 (p90) REVERT: B 94 PHE cc_start: 0.7551 (p90) cc_final: 0.7328 (p90) REVERT: C 94 PHE cc_start: 0.7555 (p90) cc_final: 0.6948 (p90) REVERT: D 44 THR cc_start: 0.8377 (m) cc_final: 0.8018 (p) REVERT: D 94 PHE cc_start: 0.7651 (p90) cc_final: 0.7199 (p90) REVERT: E 38 LEU cc_start: 0.8895 (tp) cc_final: 0.8662 (tm) REVERT: E 44 THR cc_start: 0.8485 (m) cc_final: 0.8179 (p) REVERT: F 44 THR cc_start: 0.8637 (m) cc_final: 0.8226 (p) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.0498 time to fit residues: 64.7177 Evaluate side-chains 58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.170 Angle : 0.690 9.826 3580 Z= 0.315 Chirality : 0.053 0.126 462 Planarity : 0.002 0.012 440 Dihedral : 5.034 43.910 398 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.38 % Allowed : 18.94 % Favored : 80.68 % 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: -2.05 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.010 0.002 PHE E 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.280 Fit side-chains REVERT: A 94 PHE cc_start: 0.7575 (p90) cc_final: 0.7117 (p90) REVERT: B 94 PHE cc_start: 0.7548 (p90) cc_final: 0.7266 (p90) REVERT: C 94 PHE cc_start: 0.7546 (p90) cc_final: 0.6942 (p90) REVERT: D 44 THR cc_start: 0.8410 (m) cc_final: 0.8062 (p) REVERT: D 94 PHE cc_start: 0.7643 (p90) cc_final: 0.7184 (p90) REVERT: E 38 LEU cc_start: 0.8900 (tp) cc_final: 0.8669 (tm) REVERT: E 44 THR cc_start: 0.8475 (m) cc_final: 0.8113 (p) REVERT: F 44 THR cc_start: 0.8623 (m) cc_final: 0.8184 (p) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.0302 time to fit residues: 64.4936 Evaluate side-chains 61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 2640 Z= 0.505 Angle : 0.933 13.481 3580 Z= 0.450 Chirality : 0.062 0.154 462 Planarity : 0.003 0.011 440 Dihedral : 5.894 38.678 398 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.38 % Allowed : 19.32 % Favored : 80.30 % 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: -2.41 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.012 0.002 PHE E 94 TYR 0.004 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.283 Fit side-chains REVERT: A 94 PHE cc_start: 0.7582 (p90) cc_final: 0.7130 (p90) REVERT: C 94 PHE cc_start: 0.7492 (p90) cc_final: 0.6947 (p90) REVERT: D 44 THR cc_start: 0.8563 (m) cc_final: 0.8135 (p) REVERT: D 94 PHE cc_start: 0.7677 (p90) cc_final: 0.7161 (p90) REVERT: E 44 THR cc_start: 0.8380 (m) cc_final: 0.7870 (p) REVERT: F 44 THR cc_start: 0.8557 (m) cc_final: 0.8000 (p) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 1.1595 time to fit residues: 74.7911 Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.149694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.115614 restraints weight = 12104.778| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.44 r_work: 0.3606 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2640 Z= 0.216 Angle : 0.776 11.656 3580 Z= 0.353 Chirality : 0.054 0.129 462 Planarity : 0.002 0.014 440 Dihedral : 5.279 43.132 398 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 19.32 % Favored : 80.68 % 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: -2.25 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.013 0.002 PHE E 94 TYR 0.004 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.71 seconds wall clock time: 32 minutes 33.44 seconds (1953.44 seconds total)