Starting phenix.real_space_refine on Wed Sep 17 20:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz4_32220/09_2025/7vz4_32220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz4_32220/09_2025/7vz4_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_2025/7vz4_32220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2025/7vz4_32220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2025/7vz4_32220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz4_32220/09_2025/7vz4_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-2.0-5805/lib/python3.9/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: 3.22, per 1000 atoms: 0.27 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: 1.15 Conformation dependent library (CDL) restraints added in 343.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.49 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: 2.82 Time building geometry restraints manager: 1.50 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=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" O3' DA J -1 " pdb=" P DT J 0 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.45e+01 bond pdb=" O3' DT I 1 " pdb=" P DC I 2 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 bond pdb=" C ARG E 42 " pdb=" N PRO E 43 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 12639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 14552 1.39 - 2.78: 3232 2.78 - 4.17: 487 4.17 - 5.57: 38 5.57 - 6.96: 10 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: 1115 0.052 - 0.105: 565 0.105 - 0.157: 303 0.157 - 0.210: 79 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.180 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:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.010 0.057 12644 Z= 0.695 Angle : 1.175 6.958 18319 Z= 0.890 Chirality : 0.079 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 aren 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 covalent geometry : bond 0.00990 (12644) covalent geometry : angle 1.17484 (18319) hydrogen bonds : bond 0.13905 ( 784) hydrogen bonds : angle 7.52277 ( 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 : 0.341 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 1.2048 time to fit residues: 221.7141 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147821 restraints weight = 7541.168| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.36 r_work: 0.3322 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 12644 Z= 0.174 Angle : 0.587 5.059 18319 Z= 0.363 Chirality : 0.035 0.153 2082 Planarity : 0.004 0.031 1316 Dihedral : 30.874 85.260 3992 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.65 % Allowed : 9.55 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.30), residues: 730 helix: 2.59 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.11 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.013 0.002 TYR C 57 PHE 0.008 0.001 PHE A 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (12644) covalent geometry : angle 0.58688 (18319) hydrogen bonds : bond 0.05143 ( 784) hydrogen bonds : angle 3.13961 ( 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 146 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.340 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 144 average time/residue: 1.2282 time to fit residues: 183.9968 Evaluate side-chains 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.175051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139735 restraints weight = 7417.176| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.50 r_work: 0.3215 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12644 Z= 0.318 Angle : 0.789 5.940 18319 Z= 0.468 Chirality : 0.046 0.246 2082 Planarity : 0.007 0.047 1316 Dihedral : 30.963 83.249 3992 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.46 % Allowed : 7.44 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.29), residues: 730 helix: 2.32 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 42 TYR 0.019 0.003 TYR C 57 PHE 0.017 0.004 PHE A 84 HIS 0.012 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00706 (12644) covalent geometry : angle 0.78901 (18319) hydrogen bonds : bond 0.07280 ( 784) hydrogen bonds : angle 3.51558 ( 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 142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 135 average time/residue: 1.2748 time to fit residues: 178.7846 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 : 0.328 ------------------------------------------------------------------------------- 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: 3.9990 chunk 86 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN E 68 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140577 restraints weight = 7405.309| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.42 r_work: 0.3229 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12644 Z= 0.260 Angle : 0.711 5.478 18319 Z= 0.427 Chirality : 0.042 0.200 2082 Planarity : 0.006 0.041 1316 Dihedral : 30.817 80.633 3992 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.94 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 aren not related in a simple way. whole: 2.67 (0.29), residues: 730 helix: 2.40 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.017 0.002 TYR C 57 PHE 0.013 0.003 PHE E 84 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00569 (12644) covalent geometry : angle 0.71099 (18319) hydrogen bonds : bond 0.06553 ( 784) hydrogen bonds : angle 3.39858 ( 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 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 133 average time/residue: 1.1956 time to fit residues: 165.3783 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 : 0.311 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4002 r_free = 0.4002 target = 0.177467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142760 restraints weight = 7476.111| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 0.39 r_work: 0.3256 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12644 Z= 0.187 Angle : 0.630 5.312 18319 Z= 0.386 Chirality : 0.038 0.129 2082 Planarity : 0.004 0.035 1316 Dihedral : 30.850 79.799 3992 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.13 % Allowed : 7.44 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.29), residues: 730 helix: 2.59 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.15 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 42 TYR 0.013 0.002 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00390 (12644) covalent geometry : angle 0.63035 (18319) hydrogen bonds : bond 0.05656 ( 784) hydrogen bonds : angle 3.21014 ( 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 140 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 135 average time/residue: 1.2848 time to fit residues: 180.1913 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 : 0.322 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 47 GLN E 68 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 = 0.3998 r_free = 0.3998 target = 0.177110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144527 restraints weight = 7421.207| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 0.38 r_work: 0.3252 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12644 Z= 0.206 Angle : 0.642 5.007 18319 Z= 0.390 Chirality : 0.038 0.135 2082 Planarity : 0.005 0.035 1316 Dihedral : 30.689 78.524 3992 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.13 % Allowed : 7.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.29), residues: 730 helix: 2.59 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 188 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 0.012 0.002 PHE E 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00438 (12644) covalent geometry : angle 0.64199 (18319) hydrogen bonds : bond 0.05830 ( 784) hydrogen bonds : angle 3.22978 ( 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 141 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 136 average time/residue: 1.2951 time to fit residues: 183.0043 Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 47 GLN E 68 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 = 0.3997 r_free = 0.3997 target = 0.176938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142048 restraints weight = 7405.048| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 0.39 r_work: 0.3247 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12644 Z= 0.208 Angle : 0.651 5.740 18319 Z= 0.393 Chirality : 0.038 0.139 2082 Planarity : 0.005 0.035 1316 Dihedral : 30.602 74.916 3992 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.93 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.29), residues: 730 helix: 2.58 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.07 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.015 0.002 TYR C 57 PHE 0.013 0.002 PHE E 67 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (12644) covalent geometry : angle 0.65097 (18319) hydrogen bonds : bond 0.05895 ( 784) hydrogen bonds : angle 3.22965 ( 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 140 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 136 average time/residue: 1.2679 time to fit residues: 179.1960 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 : 0.316 ------------------------------------------------------------------------------- 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: 8.9990 chunk 63 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 0.0970 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN D 47 GLN E 68 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142014 restraints weight = 7341.968| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.38 r_work: 0.3238 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12644 Z= 0.273 Angle : 0.738 6.213 18319 Z= 0.439 Chirality : 0.043 0.203 2082 Planarity : 0.006 0.040 1316 Dihedral : 30.684 74.069 3992 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 8.90 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.29), residues: 730 helix: 2.43 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.07 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.018 0.002 TYR C 57 PHE 0.013 0.003 PHE A 84 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00599 (12644) covalent geometry : angle 0.73832 (18319) hydrogen bonds : bond 0.06760 ( 784) hydrogen bonds : angle 3.41165 ( 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 139 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 135 average time/residue: 1.2865 time to fit residues: 180.4493 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 : 0.312 ------------------------------------------------------------------------------- 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: 8.9990 chunk 63 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3993 r_free = 0.3993 target = 0.176522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142238 restraints weight = 7366.232| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.39 r_work: 0.3235 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12644 Z= 0.208 Angle : 0.669 7.087 18319 Z= 0.405 Chirality : 0.039 0.148 2082 Planarity : 0.005 0.034 1316 Dihedral : 30.711 73.922 3992 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.29), residues: 730 helix: 2.49 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.013 0.002 TYR G 57 PHE 0.014 0.002 PHE E 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00443 (12644) covalent geometry : angle 0.66858 (18319) hydrogen bonds : bond 0.06017 ( 784) hydrogen bonds : angle 3.25919 ( 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 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 133 average time/residue: 1.2893 time to fit residues: 178.1741 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 : 0.385 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3993 r_free = 0.3993 target = 0.176504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142120 restraints weight = 7384.513| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.39 r_work: 0.3243 rms_B_bonded: 1.71 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: 0.8435 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12644 Z= 0.216 Angle : 0.675 7.138 18319 Z= 0.406 Chirality : 0.039 0.147 2082 Planarity : 0.005 0.035 1316 Dihedral : 30.660 73.595 3992 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.97 % Allowed : 8.58 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.29), residues: 730 helix: 2.54 (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 0.006 0.001 ARG E 42 TYR 0.015 0.002 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (12644) covalent geometry : angle 0.67509 (18319) hydrogen bonds : bond 0.06037 ( 784) hydrogen bonds : angle 3.26157 ( 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 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 130 average time/residue: 1.2958 time to fit residues: 175.0715 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 : 0.323 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3995 r_free = 0.3995 target = 0.176689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141672 restraints weight = 7443.084| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.39 r_work: 0.3250 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12644 Z= 0.207 Angle : 0.666 7.477 18319 Z= 0.402 Chirality : 0.039 0.141 2082 Planarity : 0.005 0.034 1316 Dihedral : 30.655 73.458 3992 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.97 % Allowed : 8.58 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.29), residues: 730 helix: 2.55 (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 0.012 0.001 ARG A 42 TYR 0.015 0.002 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (12644) covalent geometry : angle 0.66571 (18319) hydrogen bonds : bond 0.05938 ( 784) hydrogen bonds : angle 3.23823 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6952.35 seconds wall clock time: 118 minutes 25.25 seconds (7105.25 seconds total)