Starting phenix.real_space_refine on Fri Sep 11 19:50:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2026/7vz4_32220.map" } resolution = 1.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 14 5.16 5 C 6538 2.51 5 N 2223 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11843 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.49, per 1000 atoms: 0.21 Number of scatterers: 11843 At special positions: 0 Unit cell: (120.25, 73.45, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 288 15.00 O 2780 8.00 N 2223 7.00 C 6538 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: 0.77 Conformation dependent library (CDL) restraints added in 216.4 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.7% alpha, 3.2% beta 145 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.094A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.093A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.088A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.485A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.088A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1773 1.33 - 1.45: 4672 1.45 - 1.57: 5599 1.57 - 1.69: 576 1.69 - 1.81: 24 Bond restraints: 12644 Sorted by residual: bond pdb=" O3' DA J -1 " pdb=" P DT J 0 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.26e+01 bond pdb=" O3' DT I 1 " pdb=" P DC I 2 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.20e-02 6.94e+03 2.20e+01 bond pdb=" O3' DT J 1 " pdb=" P DC J 2 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" O3' DG I 63 " pdb=" P DG I 64 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.20e-02 6.94e+03 1.80e+01 bond pdb=" O3' DG J 63 " pdb=" P DG J 64 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.20e-02 6.94e+03 1.76e+01 ... (remaining 12639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 14826 1.39 - 2.78: 3007 2.78 - 4.17: 447 4.17 - 5.57: 31 5.57 - 6.96: 8 Bond angle restraints: 18319 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 112.90 106.65 6.25 9.60e-01 1.09e+00 4.23e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.90 106.69 6.21 9.60e-01 1.09e+00 4.19e+01 angle pdb=" N GLN G 24 " pdb=" CA GLN G 24 " pdb=" C GLN G 24 " ideal model delta sigma weight residual 113.23 107.67 5.56 1.24e+00 6.50e-01 2.01e+01 angle pdb=" N GLN C 24 " pdb=" CA GLN C 24 " pdb=" C GLN C 24 " ideal model delta sigma weight residual 113.23 107.69 5.54 1.24e+00 6.50e-01 2.00e+01 angle pdb=" N LYS F 79 " pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 113.30 107.82 5.48 1.34e+00 5.57e-01 1.67e+01 ... (remaining 18314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 4106 16.80 - 33.61: 1082 33.61 - 50.41: 1168 50.41 - 67.21: 464 67.21 - 84.02: 20 Dihedral angle restraints: 6840 sinusoidal: 4688 harmonic: 2152 Sorted by residual: dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.77 44.77 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.76 44.76 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " pdb=" OD1 ASP C 90 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.105: 629 0.105 - 0.157: 255 0.157 - 0.210: 74 0.210 - 0.262: 20 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LEU F 97 " pdb=" N LEU F 97 " pdb=" C LEU F 97 " pdb=" CB LEU F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2079 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 47 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.83e+00 pdb=" N9 DA J 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA J 47 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA J 47 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 47 " -0.011 2.00e-02 2.50e+03 pdb=" N6 DA J 47 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA J 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.022 2.00e-02 2.50e+03 9.98e-03 2.74e+00 pdb=" N9 DA I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " 0.022 2.00e-02 2.50e+03 9.72e-03 2.60e+00 pdb=" N9 DA I -54 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " 0.008 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " -0.003 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 754 2.71 - 3.26: 9628 3.26 - 3.81: 22742 3.81 - 4.35: 31188 4.35 - 4.90: 41308 Nonbonded interactions: 105620 Sorted by model distance: nonbonded pdb=" NH1 ARG G 11 " pdb=" O2 DT J -42 " model vdw 2.167 3.120 nonbonded pdb=" NH1 ARG C 11 " pdb=" O2 DT I -42 " model vdw 2.169 3.120 nonbonded pdb=" CB SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.469 3.440 nonbonded pdb=" CB SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.469 3.440 nonbonded pdb=" O5' DG I -58 " pdb=" O4' DG I -58 " model vdw 2.503 2.432 ... (remaining 105615 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.500 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.009 0.057 12644 Z= 0.705 Angle : 1.122 6.958 18319 Z= 0.893 Chirality : 0.077 0.262 2082 Planarity : 0.003 0.013 1316 Dihedral : 28.811 84.018 5456 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.97 % Allowed : 9.71 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 730 helix: 0.29 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.013 0.002 TYR G 57 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.70 (12644) covalent geometry : angle 1.12238 / 0.89 (18319) hydrogen bonds : bond 0.13905 / 9.63 ( 784) hydrogen bonds : angle 7.52277 / 5.47 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.269 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 1.0136 time to fit residues: 187.3818 Evaluate side-chains 132 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN E 68 GLN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.147240 restraints weight = 7547.150| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 0.39 r_work: 0.3324 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12644 Z= 0.151 Angle : 0.741 7.220 18319 Z= 0.412 Chirality : 0.051 0.245 2082 Planarity : 0.004 0.038 1316 Dihedral : 31.383 81.494 3992 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.29), residues: 730 helix: 2.46 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 42 TYR 0.014 0.002 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.15 (12644) covalent geometry : angle 0.74051 / 0.41 (18319) hydrogen bonds : bond 0.05787 / 3.99 ( 784) hydrogen bonds : angle 3.19055 / 2.41 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 1.0602 time to fit residues: 151.4400 Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139992 restraints weight = 7376.419| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 0.44 r_work: 0.3216 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 12644 Z= 0.306 Angle : 1.001 10.517 18319 Z= 0.535 Chirality : 0.064 0.269 2082 Planarity : 0.008 0.056 1316 Dihedral : 31.306 80.978 3992 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.13 % Allowed : 7.12 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.29), residues: 730 helix: 2.25 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 42 TYR 0.023 0.003 TYR C 57 PHE 0.019 0.004 PHE A 84 HIS 0.014 0.004 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.31 (12644) covalent geometry : angle 1.00051 / 0.54 (18319) hydrogen bonds : bond 0.08109 / 5.57 ( 784) hydrogen bonds : angle 3.66167 / 2.74 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 130 average time/residue: 1.1177 time to fit residues: 151.4198 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.175446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140041 restraints weight = 7403.639| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 0.38 r_work: 0.3226 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12644 Z= 0.221 Angle : 0.852 9.112 18319 Z= 0.470 Chirality : 0.056 0.310 2082 Planarity : 0.006 0.041 1316 Dihedral : 31.217 80.795 3992 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 5.83 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.29), residues: 730 helix: 2.34 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.15 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 42 TYR 0.020 0.002 TYR C 57 PHE 0.014 0.003 PHE A 84 HIS 0.010 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.22 (12644) covalent geometry : angle 0.85186 / 0.47 (18319) hydrogen bonds : bond 0.06950 / 4.77 ( 784) hydrogen bonds : angle 3.45956 / 2.59 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 132 average time/residue: 1.0797 time to fit residues: 148.5385 Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142435 restraints weight = 7495.201| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 0.39 r_work: 0.3246 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12644 Z= 0.166 Angle : 0.762 8.039 18319 Z= 0.428 Chirality : 0.052 0.264 2082 Planarity : 0.005 0.036 1316 Dihedral : 31.229 79.902 3992 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 6.63 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.29), residues: 730 helix: 2.55 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.09 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.015 0.002 TYR C 57 PHE 0.014 0.002 PHE E 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.17 (12644) covalent geometry : angle 0.76196 / 0.43 (18319) hydrogen bonds : bond 0.06130 / 4.22 ( 784) hydrogen bonds : angle 3.28395 / 2.46 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 131 average time/residue: 1.0720 time to fit residues: 146.1401 Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142427 restraints weight = 7411.051| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 0.37 r_work: 0.3252 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12644 Z= 0.179 Angle : 0.767 8.571 18319 Z= 0.431 Chirality : 0.051 0.244 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.149 79.803 3992 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.29 % Allowed : 6.80 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.29), residues: 730 helix: 2.50 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (12644) covalent geometry : angle 0.76750 / 0.43 (18319) hydrogen bonds : bond 0.06323 / 4.34 ( 784) hydrogen bonds : angle 3.32025 / 2.49 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 1.0736 time to fit residues: 148.7549 Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141367 restraints weight = 7409.932| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.37 r_work: 0.3247 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12644 Z= 0.178 Angle : 0.765 8.457 18319 Z= 0.429 Chirality : 0.050 0.244 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.122 79.341 3992 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 6.96 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.29), residues: 730 helix: 2.52 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 35 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.18 (12644) covalent geometry : angle 0.76482 / 0.43 (18319) hydrogen bonds : bond 0.06271 / 4.31 ( 784) hydrogen bonds : angle 3.30355 / 2.47 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 132 average time/residue: 1.0697 time to fit residues: 147.0749 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139490 restraints weight = 7361.976| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 0.37 r_work: 0.3222 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12644 Z= 0.237 Angle : 0.879 9.813 18319 Z= 0.481 Chirality : 0.057 0.257 2082 Planarity : 0.006 0.045 1316 Dihedral : 31.123 78.497 3992 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.97 % Allowed : 7.12 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.29), residues: 730 helix: 2.32 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.018 0.002 TYR C 57 PHE 0.012 0.003 PHE E 67 HIS 0.009 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.24 (12644) covalent geometry : angle 0.87899 / 0.48 (18319) hydrogen bonds : bond 0.07276 / 5.00 ( 784) hydrogen bonds : angle 3.50158 / 2.62 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 130 average time/residue: 1.0535 time to fit residues: 142.7526 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141989 restraints weight = 7396.193| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 0.36 r_work: 0.3254 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12644 Z= 0.170 Angle : 0.785 8.638 18319 Z= 0.439 Chirality : 0.053 0.243 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.162 77.874 3992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.97 % Allowed : 7.12 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.29), residues: 730 helix: 2.42 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 35 TYR 0.013 0.002 TYR G 57 PHE 0.015 0.002 PHE A 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.17 (12644) covalent geometry : angle 0.78500 / 0.44 (18319) hydrogen bonds : bond 0.06277 / 4.32 ( 784) hydrogen bonds : angle 3.32568 / 2.49 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 130 average time/residue: 1.0725 time to fit residues: 145.3045 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN D 47 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141110 restraints weight = 7413.812| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.38 r_work: 0.3242 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12644 Z= 0.182 Angle : 0.790 8.590 18319 Z= 0.440 Chirality : 0.052 0.248 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.131 78.263 3992 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 6.96 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.29), residues: 730 helix: 2.47 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.05 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.18 (12644) covalent geometry : angle 0.78989 / 0.44 (18319) hydrogen bonds : bond 0.06367 / 4.38 ( 784) hydrogen bonds : angle 3.33535 / 2.50 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8983 (mmm) cc_final: 0.8772 (mmm) outliers start: 6 outliers final: 6 residues processed: 127 average time/residue: 1.0577 time to fit residues: 139.9274 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 97 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN D 47 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142608 restraints weight = 7506.622| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 0.37 r_work: 0.3260 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12644 Z= 0.155 Angle : 0.744 7.943 18319 Z= 0.422 Chirality : 0.050 0.229 2082 Planarity : 0.004 0.034 1316 Dihedral : 31.153 78.072 3992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.65 % Allowed : 7.28 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.29), residues: 730 helix: 2.50 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.10 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 92 TYR 0.012 0.002 TYR F 88 PHE 0.015 0.002 PHE E 67 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.15 (12644) covalent geometry : angle 0.74443 / 0.42 (18319) hydrogen bonds : bond 0.05869 / 4.05 ( 784) hydrogen bonds : angle 3.23793 / 2.42 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5980.61 seconds wall clock time: 101 minutes 57.19 seconds (6117.19 seconds total)