Starting phenix.real_space_refine on Sat Dec 28 15:07:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.map" model { file = "/net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zzy_15041/12_2024/7zzy_15041.cif" } resolution = 3.3 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= 0.013 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5600 2.51 5 N 1488 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "G" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "E" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "C" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "H" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "B" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "D" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "F" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AMET A 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 46 " occ=0.50 residue: pdb=" N AMET G 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET G 46 " occ=0.50 residue: pdb=" N AMET E 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET E 46 " occ=0.50 residue: pdb=" N AMET C 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 46 " occ=0.50 residue: pdb=" N AMET H 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET H 46 " occ=0.50 residue: pdb=" N AMET B 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 46 " occ=0.50 residue: pdb=" N AMET D 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET D 46 " occ=0.50 residue: pdb=" N AMET F 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET F 46 " occ=0.50 Time building chain proxies: 9.43, per 1000 atoms: 1.07 Number of scatterers: 8784 At special positions: 0 Unit cell: (97.65, 97.65, 80.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1648 8.00 N 1488 7.00 C 5600 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: 2.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 48.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.584A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.712A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.989A pdb=" N GLN A 119 " --> pdb=" O TRP A 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 Processing helix chain 'G' and resid 28 through 45 removed outlier: 3.577A pdb=" N GLU G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG G 44 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 45 " --> pdb=" O MET G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 68 removed outlier: 3.740A pdb=" N ILE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.515A pdb=" N LEU G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN G 119 " --> pdb=" O TRP G 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 Processing helix chain 'E' and resid 28 through 45 removed outlier: 3.594A pdb=" N GLU E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 44 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 45 " --> pdb=" O MET E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 68 removed outlier: 3.742A pdb=" N ILE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.533A pdb=" N LEU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN E 119 " --> pdb=" O TRP E 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 28 through 45 removed outlier: 3.598A pdb=" N GLU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.724A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.954A pdb=" N GLN C 119 " --> pdb=" O TRP C 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 Processing helix chain 'H' and resid 28 through 45 removed outlier: 3.599A pdb=" N GLU H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 45 " --> pdb=" O MET H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 68 removed outlier: 3.718A pdb=" N ILE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 119 removed outlier: 3.536A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN H 119 " --> pdb=" O TRP H 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.593A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.838A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.537A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 119 " --> pdb=" O TRP B 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 28 through 45 removed outlier: 3.603A pdb=" N GLU D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.720A pdb=" N ILE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.536A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 Processing helix chain 'F' and resid 28 through 45 removed outlier: 3.577A pdb=" N GLU F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 44 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.740A pdb=" N ILE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.551A pdb=" N LEU F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN F 119 " --> pdb=" O TRP F 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 Processing sheet with id=AA2, first strand: chain 'G' and resid 71 through 77 removed outlier: 3.503A pdb=" N ARG G 150 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 77 Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 77 Processing sheet with id=AA5, first strand: chain 'H' and resid 71 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 77 Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AA8, first strand: chain 'F' and resid 71 through 77 497 hydrogen bonds defined for protein. 1395 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: 2.50 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2881 1.34 - 1.46: 1496 1.46 - 1.58: 4463 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8928 Sorted by residual: bond pdb=" CB PRO F 99 " pdb=" CG PRO F 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.23e-01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.19e-01 bond pdb=" CB PRO E 99 " pdb=" CG PRO E 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.19e-01 bond pdb=" CB PRO H 99 " pdb=" CG PRO H 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.10e-01 bond pdb=" CB PRO D 99 " pdb=" CG PRO D 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.04e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 11944 1.36 - 2.72: 126 2.72 - 4.08: 68 4.08 - 5.44: 12 5.44 - 6.80: 2 Bond angle restraints: 12152 Sorted by residual: angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 111.56 114.39 -2.83 1.01e+00 9.80e-01 7.83e+00 angle pdb=" N GLY G 70 " pdb=" CA GLY G 70 " pdb=" C GLY G 70 " ideal model delta sigma weight residual 111.56 114.32 -2.76 1.01e+00 9.80e-01 7.44e+00 angle pdb=" N GLY F 70 " pdb=" CA GLY F 70 " pdb=" C GLY F 70 " ideal model delta sigma weight residual 111.56 114.31 -2.75 1.01e+00 9.80e-01 7.43e+00 angle pdb=" N GLY D 70 " pdb=" CA GLY D 70 " pdb=" C GLY D 70 " ideal model delta sigma weight residual 110.60 114.27 -3.67 1.46e+00 4.69e-01 6.34e+00 angle pdb=" CA LEU E 76 " pdb=" CB LEU E 76 " pdb=" CG LEU E 76 " ideal model delta sigma weight residual 116.30 123.10 -6.80 3.50e+00 8.16e-02 3.77e+00 ... (remaining 12147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4697 17.37 - 34.75: 484 34.75 - 52.12: 117 52.12 - 69.50: 25 69.50 - 86.87: 29 Dihedral angle restraints: 5352 sinusoidal: 2200 harmonic: 3152 Sorted by residual: dihedral pdb=" CA BMET G 46 " pdb=" CB BMET G 46 " pdb=" CG BMET G 46 " pdb=" SD BMET G 46 " ideal model delta sinusoidal sigma weight residual 180.00 130.53 49.47 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" CA BMET F 46 " pdb=" CB BMET F 46 " pdb=" CG BMET F 46 " pdb=" SD BMET F 46 " ideal model delta sinusoidal sigma weight residual 180.00 130.60 49.40 3 1.50e+01 4.44e-03 8.77e+00 dihedral pdb=" CB ARG D 35 " pdb=" CG ARG D 35 " pdb=" CD ARG D 35 " pdb=" NE ARG D 35 " ideal model delta sinusoidal sigma weight residual -60.00 -109.12 49.12 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 921 0.028 - 0.057: 344 0.057 - 0.085: 78 0.085 - 0.114: 61 0.114 - 0.142: 12 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CG LEU A 63 " pdb=" CB LEU A 63 " pdb=" CD1 LEU A 63 " pdb=" CD2 LEU A 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CG LEU H 63 " pdb=" CB LEU H 63 " pdb=" CD1 LEU H 63 " pdb=" CD2 LEU H 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE E 85 " pdb=" N ILE E 85 " pdb=" C ILE E 85 " pdb=" CB ILE E 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1413 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 140 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO F 141 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO F 141 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 141 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 140 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 141 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 141 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 141 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 140 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO G 141 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " 0.016 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1250 2.77 - 3.30: 7733 3.30 - 3.84: 13861 3.84 - 4.37: 15448 4.37 - 4.90: 28821 Nonbonded interactions: 67113 Sorted by model distance: nonbonded pdb=" OD2 ASP F 80 " pdb=" OG SER F 82 " model vdw 2.238 3.040 nonbonded pdb=" OD2 ASP H 80 " pdb=" OG SER H 82 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP B 80 " pdb=" OG SER B 82 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP D 80 " pdb=" OG SER D 82 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP E 80 " pdb=" OG SER E 82 " model vdw 2.248 3.040 ... (remaining 67108 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 6 through 45 or resid 47 through 151)) selection = (chain 'B' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'C' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'D' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'E' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'F' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'G' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'H' and (resid 6 through 45 or resid 47 through 151)) } 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: 3.250 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.790 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.002 0.025 8928 Z= 0.130 Angle : 0.470 6.800 12152 Z= 0.240 Chirality : 0.036 0.142 1416 Planarity : 0.004 0.030 1552 Dihedral : 16.507 86.874 3320 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.09 (0.25), residues: 1080 helix: 1.91 (0.23), residues: 488 sheet: 0.90 (0.31), residues: 232 loop : -1.09 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 103 HIS 0.001 0.000 HIS C 87 PHE 0.002 0.000 PHE G 10 TYR 0.004 0.001 TYR A 112 ARG 0.002 0.000 ARG G 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2235 time to fit residues: 66.5555 Evaluate side-chains 162 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8928 Z= 0.216 Angle : 0.640 7.107 12152 Z= 0.332 Chirality : 0.040 0.143 1416 Planarity : 0.004 0.030 1552 Dihedral : 3.364 13.491 1192 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.24 % Allowed : 11.78 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.35 (0.25), residues: 1080 helix: 2.19 (0.22), residues: 488 sheet: 1.07 (0.31), residues: 232 loop : -1.09 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 69 HIS 0.001 0.001 HIS E 87 PHE 0.003 0.001 PHE B 10 TYR 0.006 0.001 TYR G 112 ARG 0.002 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 1.247 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 181 average time/residue: 0.2230 time to fit residues: 55.3484 Evaluate side-chains 146 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.7982 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 8928 Z= 0.385 Angle : 0.749 12.072 12152 Z= 0.387 Chirality : 0.043 0.216 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.899 17.291 1192 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.03 % Allowed : 15.29 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.21 (0.25), residues: 1080 helix: 2.04 (0.23), residues: 488 sheet: 1.04 (0.30), residues: 232 loop : -1.14 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.003 0.002 HIS G 87 PHE 0.016 0.003 PHE A 123 TYR 0.010 0.002 TYR B 126 ARG 0.003 0.000 ARG G 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 1.024 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 171 average time/residue: 0.2212 time to fit residues: 52.1460 Evaluate side-chains 149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8928 Z= 0.227 Angle : 0.721 7.693 12152 Z= 0.370 Chirality : 0.043 0.199 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.821 15.761 1192 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.25 (0.25), residues: 1080 helix: 2.16 (0.23), residues: 488 sheet: 1.07 (0.30), residues: 232 loop : -1.28 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 19 HIS 0.001 0.001 HIS E 87 PHE 0.024 0.002 PHE H 123 TYR 0.015 0.001 TYR F 126 ARG 0.001 0.000 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2290 time to fit residues: 50.7351 Evaluate side-chains 149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.0000 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8928 Z= 0.214 Angle : 0.688 5.892 12152 Z= 0.358 Chirality : 0.042 0.175 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.774 13.362 1192 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.31 % Allowed : 16.32 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.34 (0.25), residues: 1080 helix: 2.24 (0.23), residues: 488 sheet: 1.16 (0.30), residues: 232 loop : -1.28 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 19 HIS 0.002 0.001 HIS G 87 PHE 0.019 0.002 PHE F 123 TYR 0.006 0.001 TYR E 112 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 1.053 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.2092 time to fit residues: 44.7939 Evaluate side-chains 147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8928 Z= 0.280 Angle : 0.722 8.337 12152 Z= 0.372 Chirality : 0.043 0.194 1416 Planarity : 0.004 0.025 1552 Dihedral : 3.692 12.719 1192 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.10 % Allowed : 17.87 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.43 (0.25), residues: 1080 helix: 2.25 (0.23), residues: 488 sheet: 1.27 (0.30), residues: 232 loop : -1.18 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.002 0.001 HIS E 87 PHE 0.018 0.002 PHE F 123 TYR 0.006 0.001 TYR F 126 ARG 0.007 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.969 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.2202 time to fit residues: 47.1342 Evaluate side-chains 146 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8928 Z= 0.223 Angle : 0.723 8.196 12152 Z= 0.372 Chirality : 0.043 0.210 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.638 12.526 1192 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.31 % Allowed : 17.15 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.51 (0.25), residues: 1080 helix: 2.30 (0.23), residues: 488 sheet: 1.33 (0.31), residues: 232 loop : -1.12 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 69 HIS 0.002 0.001 HIS H 87 PHE 0.015 0.002 PHE B 123 TYR 0.007 0.001 TYR D 112 ARG 0.005 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.964 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.2129 time to fit residues: 47.1573 Evaluate side-chains 145 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN B 15 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8928 Z= 0.236 Angle : 0.732 8.726 12152 Z= 0.375 Chirality : 0.042 0.199 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.597 12.609 1192 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.31 % Allowed : 18.29 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.63 (0.26), residues: 1080 helix: 2.39 (0.23), residues: 488 sheet: 1.38 (0.31), residues: 232 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS B 87 PHE 0.014 0.002 PHE D 123 TYR 0.006 0.001 TYR G 112 ARG 0.002 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.955 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 161 average time/residue: 0.2055 time to fit residues: 45.7247 Evaluate side-chains 150 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8928 Z= 0.247 Angle : 0.763 8.980 12152 Z= 0.390 Chirality : 0.043 0.197 1416 Planarity : 0.004 0.058 1552 Dihedral : 3.575 12.866 1192 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.31 % Allowed : 18.80 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.73 (0.26), residues: 1080 helix: 2.50 (0.23), residues: 488 sheet: 1.39 (0.31), residues: 232 loop : -1.02 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS G 87 PHE 0.012 0.002 PHE E 123 TYR 0.005 0.001 TYR D 112 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.116 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 162 average time/residue: 0.2053 time to fit residues: 45.9348 Evaluate side-chains 153 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 0.0070 chunk 8 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8928 Z= 0.268 Angle : 0.781 9.128 12152 Z= 0.402 Chirality : 0.042 0.205 1416 Planarity : 0.004 0.030 1552 Dihedral : 3.572 12.995 1192 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.52 % Allowed : 18.90 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.64 (0.26), residues: 1080 helix: 2.39 (0.23), residues: 488 sheet: 1.37 (0.32), residues: 232 loop : -1.00 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS D 87 PHE 0.011 0.002 PHE H 123 TYR 0.004 0.001 TYR C 126 ARG 0.005 0.000 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.940 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 158 average time/residue: 0.2101 time to fit residues: 45.8139 Evaluate side-chains 156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 SER Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.056464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.042062 restraints weight = 174262.651| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 9.80 r_work: 0.2479 rms_B_bonded: 8.98 restraints_weight: 2.0000 r_work: 0.2644 rms_B_bonded: 5.64 restraints_weight: 4.0000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8928 Z= 0.248 Angle : 0.788 9.108 12152 Z= 0.404 Chirality : 0.042 0.192 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.536 12.820 1192 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.31 % Allowed : 18.80 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.70 (0.26), residues: 1080 helix: 2.41 (0.22), residues: 488 sheet: 1.40 (0.32), residues: 232 loop : -0.93 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 115 HIS 0.002 0.001 HIS B 87 PHE 0.013 0.002 PHE D 123 TYR 0.006 0.001 TYR G 112 ARG 0.004 0.000 ARG F 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.98 seconds wall clock time: 40 minutes 9.06 seconds (2409.06 seconds total)