Starting phenix.real_space_refine on Mon Feb 10 21:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wmm_32615/02_2025/7wmm_32615_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wmm_32615/02_2025/7wmm_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_32615/02_2025/7wmm_32615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wmm_32615/02_2025/7wmm_32615.map" model { file = "/net/cci-nas-00/data/ceres_data/7wmm_32615/02_2025/7wmm_32615_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wmm_32615/02_2025/7wmm_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-5592/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: 3.59, per 1000 atoms: 1.37 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: 0.65 Conformation dependent library (CDL) restraints added in 647.9 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: 0.33 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: 0.55 Time building geometry restraints manager: 0.73 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 2.440 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: 0.040 Process input model: 13.210 Find NCS groups from input model: 0.070 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.660 ------------------------------------------------------------------------------- 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 : 0.289 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: 1.4034 time to fit residues: 102.9919 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=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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.144904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110394 restraints weight = 15445.886| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.75 r_work: 0.3505 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 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 : 0.232 Fit side-chains REVERT: A 94 PHE cc_start: 0.7490 (p90) cc_final: 0.6935 (p90) REVERT: C 94 PHE cc_start: 0.7487 (p90) cc_final: 0.6760 (p90) REVERT: E 38 LEU cc_start: 0.8899 (tp) cc_final: 0.8651 (tm) REVERT: E 94 PHE cc_start: 0.7870 (p90) cc_final: 0.7478 (p90) REVERT: F 44 THR cc_start: 0.8745 (m) cc_final: 0.8200 (p) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 1.1819 time to fit residues: 77.3119 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.0270 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.150752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115910 restraints weight = 15866.957| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.93 r_work: 0.3593 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2640 Z= 0.149 Angle : 0.705 10.848 3580 Z= 0.320 Chirality : 0.053 0.126 462 Planarity : 0.002 0.015 440 Dihedral : 5.281 39.919 398 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.38 % Allowed : 17.80 % 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 (0.42), 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 0.005 0.003 HIS C 50 PHE 0.007 0.002 PHE F 94 TYR 0.006 0.001 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 61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.263 Fit side-chains REVERT: A 94 PHE cc_start: 0.7526 (p90) cc_final: 0.7005 (p90) REVERT: C 94 PHE cc_start: 0.7468 (p90) cc_final: 0.6733 (p90) REVERT: D 44 THR cc_start: 0.8382 (m) cc_final: 0.8080 (p) REVERT: E 38 LEU cc_start: 0.8855 (tp) cc_final: 0.8623 (tm) REVERT: E 44 THR cc_start: 0.8613 (m) cc_final: 0.8180 (p) REVERT: E 94 PHE cc_start: 0.7898 (p90) cc_final: 0.7540 (p90) REVERT: F 44 THR cc_start: 0.8713 (m) cc_final: 0.8247 (p) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.0029 time to fit residues: 61.8341 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.148125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113264 restraints weight = 14745.935| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.81 r_work: 0.3552 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2640 Z= 0.255 Angle : 0.758 11.653 3580 Z= 0.351 Chirality : 0.055 0.132 462 Planarity : 0.002 0.013 440 Dihedral : 5.540 43.895 398 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: -2.40 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (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 F 94 TYR 0.006 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: 5 poor density : 57 time to evaluate : 0.285 Fit side-chains REVERT: A 94 PHE cc_start: 0.7541 (p90) cc_final: 0.7029 (p90) REVERT: C 94 PHE cc_start: 0.7477 (p90) cc_final: 0.6737 (p90) REVERT: D 44 THR cc_start: 0.8472 (m) cc_final: 0.8160 (p) REVERT: E 38 LEU cc_start: 0.8893 (tp) cc_final: 0.8658 (tm) REVERT: E 44 THR cc_start: 0.8577 (m) cc_final: 0.8090 (p) REVERT: E 94 PHE cc_start: 0.7863 (p90) cc_final: 0.7507 (p90) REVERT: F 44 THR cc_start: 0.8689 (m) cc_final: 0.8175 (p) outliers start: 5 outliers final: 1 residues processed: 58 average time/residue: 1.0261 time to fit residues: 61.1958 Evaluate side-chains 58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.151911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116420 restraints weight = 19702.687| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.21 r_work: 0.3597 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.137 Angle : 0.658 10.020 3580 Z= 0.298 Chirality : 0.053 0.126 462 Planarity : 0.002 0.012 440 Dihedral : 4.882 42.870 398 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.38 % Allowed : 18.18 % 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: -2.16 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.009 0.002 PHE D 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 58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.290 Fit side-chains REVERT: A 94 PHE cc_start: 0.7496 (p90) cc_final: 0.6997 (p90) REVERT: C 94 PHE cc_start: 0.7462 (p90) cc_final: 0.6747 (p90) REVERT: D 44 THR cc_start: 0.8416 (m) cc_final: 0.8139 (p) REVERT: E 38 LEU cc_start: 0.8904 (tp) cc_final: 0.8646 (tm) REVERT: E 44 THR cc_start: 0.8633 (m) cc_final: 0.8230 (p) REVERT: F 44 THR cc_start: 0.8742 (m) cc_final: 0.8306 (p) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.0355 time to fit residues: 60.6782 Evaluate side-chains 56 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112882 restraints weight = 16826.641| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.92 r_work: 0.3545 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2640 Z= 0.272 Angle : 0.765 11.591 3580 Z= 0.353 Chirality : 0.055 0.132 462 Planarity : 0.002 0.011 440 Dihedral : 5.420 43.104 398 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -2.26 (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 C 50 PHE 0.010 0.002 PHE B 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 61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.336 Fit side-chains REVERT: A 94 PHE cc_start: 0.7516 (p90) cc_final: 0.6998 (p90) REVERT: C 94 PHE cc_start: 0.7467 (p90) cc_final: 0.6797 (p90) REVERT: D 44 THR cc_start: 0.8510 (m) cc_final: 0.8192 (p) REVERT: E 38 LEU cc_start: 0.8887 (tp) cc_final: 0.8649 (tm) REVERT: E 44 THR cc_start: 0.8579 (m) cc_final: 0.8089 (p) REVERT: F 44 THR cc_start: 0.8691 (m) cc_final: 0.8176 (p) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.0533 time to fit residues: 66.0446 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 2.0098 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114998 restraints weight = 16544.039| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.86 r_work: 0.3584 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2640 Z= 0.196 Angle : 0.711 10.755 3580 Z= 0.325 Chirality : 0.054 0.128 462 Planarity : 0.002 0.011 440 Dihedral : 5.190 44.882 398 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.76 % Allowed : 18.94 % 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: -2.15 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (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 A 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: 2 poor density : 60 time to evaluate : 0.475 Fit side-chains REVERT: A 94 PHE cc_start: 0.7476 (p90) cc_final: 0.6971 (p90) REVERT: C 94 PHE cc_start: 0.7478 (p90) cc_final: 0.6883 (p90) REVERT: D 44 THR cc_start: 0.8480 (m) cc_final: 0.8186 (p) REVERT: E 38 LEU cc_start: 0.8892 (tp) cc_final: 0.8669 (tm) REVERT: E 44 THR cc_start: 0.8614 (m) cc_final: 0.8183 (p) REVERT: F 44 THR cc_start: 0.8683 (m) cc_final: 0.8208 (p) outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 1.1718 time to fit residues: 73.5019 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114810 restraints weight = 16922.725| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.98 r_work: 0.3579 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2640 Z= 0.207 Angle : 0.726 10.776 3580 Z= 0.332 Chirality : 0.054 0.128 462 Planarity : 0.002 0.010 440 Dihedral : 5.288 45.196 398 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 19.70 % 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: -2.15 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.015 0.003 PHE B 94 TYR 0.004 0.001 TYR A 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 61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.271 Fit side-chains REVERT: A 94 PHE cc_start: 0.7471 (p90) cc_final: 0.7010 (p90) REVERT: C 94 PHE cc_start: 0.7463 (p90) cc_final: 0.6847 (p90) REVERT: D 44 THR cc_start: 0.8503 (m) cc_final: 0.8185 (p) REVERT: E 38 LEU cc_start: 0.8890 (tp) cc_final: 0.8663 (tm) REVERT: E 44 THR cc_start: 0.8607 (m) cc_final: 0.8164 (p) REVERT: F 44 THR cc_start: 0.8683 (m) cc_final: 0.8182 (p) outliers start: 0 outliers final: 1 residues processed: 61 average time/residue: 1.1534 time to fit residues: 72.0769 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 : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 0.0070 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.149990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114897 restraints weight = 16922.345| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.93 r_work: 0.3582 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2163 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= 0.211 Angle : 0.730 10.772 3580 Z= 0.334 Chirality : 0.054 0.129 462 Planarity : 0.002 0.011 440 Dihedral : 5.277 45.540 398 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -2.11 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.33), 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 A 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 : 0.266 Fit side-chains REVERT: A 94 PHE cc_start: 0.7484 (p90) cc_final: 0.7040 (p90) REVERT: C 94 PHE cc_start: 0.7431 (p90) cc_final: 0.6976 (p90) REVERT: D 44 THR cc_start: 0.8480 (m) cc_final: 0.8182 (p) REVERT: E 38 LEU cc_start: 0.8893 (tp) cc_final: 0.8673 (tm) REVERT: E 44 THR cc_start: 0.8604 (m) cc_final: 0.8159 (p) REVERT: F 44 THR cc_start: 0.8670 (m) cc_final: 0.8179 (p) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.0851 time to fit residues: 67.9286 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 : 0.299 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111995 restraints weight = 16081.188| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.82 r_work: 0.3533 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2640 Z= 0.357 Angle : 0.848 12.497 3580 Z= 0.398 Chirality : 0.058 0.139 462 Planarity : 0.002 0.010 440 Dihedral : 5.641 40.811 398 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 20.08 % Favored : 79.92 % 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: -2.30 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.019 0.003 PHE B 94 TYR 0.004 0.001 TYR A 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 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.255 Fit side-chains REVERT: A 94 PHE cc_start: 0.7507 (p90) cc_final: 0.7017 (p90) REVERT: B 38 LEU cc_start: 0.8879 (tp) cc_final: 0.8640 (tp) REVERT: C 94 PHE cc_start: 0.7407 (p90) cc_final: 0.6890 (p90) REVERT: D 44 THR cc_start: 0.8561 (m) cc_final: 0.8213 (p) REVERT: E 38 LEU cc_start: 0.8898 (tp) cc_final: 0.8657 (tm) REVERT: F 44 THR cc_start: 0.8674 (m) cc_final: 0.8138 (p) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.1557 time to fit residues: 73.3489 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 0.0040 chunk 28 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.6796 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115677 restraints weight = 20099.711| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.17 r_work: 0.3586 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2640 Z= 0.183 Angle : 0.733 10.852 3580 Z= 0.333 Chirality : 0.054 0.125 462 Planarity : 0.002 0.014 440 Dihedral : 5.150 45.044 398 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 20.45 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.012 0.002 PHE E 94 TYR 0.005 0.001 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.58 seconds wall clock time: 48 minutes 46.38 seconds (2926.38 seconds total)