Starting phenix.real_space_refine on Wed Sep 25 21:32:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_32220.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_32220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_32220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_32220.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz4_32220/09_2024/7vz4_32220.cif" } resolution = 1.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.55, per 1000 atoms: 0.64 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: 2.95 Conformation dependent library (CDL) restraints added in 874.4 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: 6.65 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: 4.91 Time building geometry restraints manager: 3.50 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: 2.110 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: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- 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= 0.608 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.002 TYR G 57 ARG 0.002 0.000 ARG B 92 *********************** 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 fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 0.956 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 2.3047 time to fit residues: 425.0793 Evaluate side-chains 130 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12644 Z= 0.202 Angle : 0.608 5.515 18319 Z= 0.374 Chirality : 0.037 0.173 2082 Planarity : 0.004 0.029 1316 Dihedral : 30.918 85.413 3992 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.29), residues: 730 helix: 2.45 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.13 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.015 0.002 TYR C 57 ARG 0.006 0.001 ARG B 35 *********************** 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 147 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.924 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 143 average time/residue: 2.3933 time to fit residues: 356.6978 Evaluate side-chains 139 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12644 Z= 0.297 Angle : 0.702 5.689 18319 Z= 0.422 Chirality : 0.042 0.203 2082 Planarity : 0.005 0.036 1316 Dihedral : 30.884 83.261 3992 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.29), residues: 730 helix: 2.47 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 75 PHE 0.014 0.003 PHE A 84 TYR 0.017 0.002 TYR G 57 ARG 0.008 0.001 ARG C 42 *********************** 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 140 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 136 average time/residue: 2.5505 time to fit residues: 360.7512 Evaluate side-chains 135 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 88 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12644 Z= 0.281 Angle : 0.681 5.162 18319 Z= 0.411 Chirality : 0.040 0.201 2082 Planarity : 0.005 0.036 1316 Dihedral : 30.742 80.816 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 : 1.46 % Allowed : 8.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.29), residues: 730 helix: 2.48 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 75 PHE 0.012 0.003 PHE E 84 TYR 0.016 0.002 TYR C 57 ARG 0.007 0.001 ARG B 67 *********************** 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 144 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 137 average time/residue: 2.3631 time to fit residues: 337.1817 Evaluate side-chains 138 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 53 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12644 Z= 0.371 Angle : 0.773 5.703 18319 Z= 0.458 Chirality : 0.045 0.208 2082 Planarity : 0.006 0.044 1316 Dihedral : 30.874 77.557 3992 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.77 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 730 helix: 2.31 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS F 75 PHE 0.014 0.004 PHE A 84 TYR 0.019 0.002 TYR C 57 ARG 0.010 0.001 ARG B 67 *********************** 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 138 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 134 average time/residue: 2.4645 time to fit residues: 344.0423 Evaluate side-chains 133 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 85 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12644 Z= 0.368 Angle : 0.768 5.616 18319 Z= 0.455 Chirality : 0.045 0.214 2082 Planarity : 0.006 0.044 1316 Dihedral : 30.805 75.501 3992 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.29), residues: 730 helix: 2.27 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.13 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 75 PHE 0.013 0.003 PHE E 84 TYR 0.019 0.002 TYR C 57 ARG 0.009 0.001 ARG B 35 *********************** 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 137 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 2.4910 time to fit residues: 342.3267 Evaluate side-chains 132 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12644 Z= 0.201 Angle : 0.635 5.620 18319 Z= 0.388 Chirality : 0.038 0.127 2082 Planarity : 0.004 0.035 1316 Dihedral : 30.842 74.373 3992 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 6.80 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.29), residues: 730 helix: 2.56 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.016 0.002 PHE E 67 TYR 0.014 0.002 TYR D 40 ARG 0.004 0.001 ARG H 86 *********************** 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 fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 136 average time/residue: 2.5718 time to fit residues: 364.1502 Evaluate side-chains 136 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 37 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.2644 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12644 Z= 0.214 Angle : 0.634 5.895 18319 Z= 0.385 Chirality : 0.037 0.130 2082 Planarity : 0.004 0.035 1316 Dihedral : 30.701 74.916 3992 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.44 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.29), residues: 730 helix: 2.61 (0.21), residues: 542 sheet: None (None), residues: 0 loop : 0.00 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.014 0.002 TYR C 57 ARG 0.004 0.001 ARG A 42 *********************** 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 137 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 133 average time/residue: 2.4547 time to fit residues: 339.9252 Evaluate side-chains 135 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 82 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12644 Z= 0.195 Angle : 0.623 7.326 18319 Z= 0.379 Chirality : 0.036 0.126 2082 Planarity : 0.004 0.035 1316 Dihedral : 30.691 74.882 3992 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 8.09 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.29), residues: 730 helix: 2.72 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE A 67 TYR 0.012 0.002 TYR C 57 ARG 0.004 0.000 ARG E 42 *********************** 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 139 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 135 average time/residue: 2.5649 time to fit residues: 360.2291 Evaluate side-chains 138 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 93 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12644 Z= 0.196 Angle : 0.613 6.734 18319 Z= 0.375 Chirality : 0.036 0.127 2082 Planarity : 0.004 0.035 1316 Dihedral : 30.663 74.876 3992 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.29), residues: 730 helix: 2.69 (0.21), residues: 542 sheet: None (None), residues: 0 loop : 0.03 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.013 0.001 TYR C 57 ARG 0.003 0.000 ARG B 67 ********************** 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 139 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 135 average time/residue: 2.5592 time to fit residues: 359.5198 Evaluate side-chains 137 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 82 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.177599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142677 restraints weight = 7374.038| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.39 r_work: 0.3257 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2521 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= 0.223 Angle : 0.638 7.412 18319 Z= 0.386 Chirality : 0.038 0.128 2082 Planarity : 0.005 0.035 1316 Dihedral : 30.552 72.219 3992 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 8.41 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.29), residues: 730 helix: 2.63 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 75 PHE 0.012 0.002 PHE A 67 TYR 0.015 0.002 TYR C 57 ARG 0.006 0.001 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.42 seconds wall clock time: 102 minutes 19.05 seconds (6139.05 seconds total)