Starting phenix.real_space_refine on Sat Dec 9 07:38:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/12_2023/7vbm_31882.pdb" } resolution = 3.4 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 251 5.49 5 S 14 5.16 5 C 5799 2.51 5 N 1944 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10475 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 712 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 603 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 719 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "H" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2566 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2597 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Time building chain proxies: 5.89, per 1000 atoms: 0.56 Number of scatterers: 10475 At special positions: 0 Unit cell: (116.6, 94.34, 124.02, 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 251 15.00 O 2467 8.00 N 1944 7.00 C 5799 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 - 3.50 Amino acid : False - 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: 5.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 76.4% alpha, 3.0% beta 117 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.568A pdb=" N CYS A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.552A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.621A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.729A pdb=" N LEU C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.597A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.651A pdb=" N VAL D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.763A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.784A pdb=" N THR E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.736A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.835A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 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 removed outlier: 3.596A pdb=" N VAL H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.835A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.066A pdb=" N CYS 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.654A 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 101 through 102 removed outlier: 6.926A 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: 7.105A pdb=" N CYS 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: 7.545A 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 78 380 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 612 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 6.09 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: 1717 1.33 - 1.45: 3846 1.45 - 1.57: 5084 1.57 - 1.69: 502 1.69 - 1.81: 22 Bond restraints: 11171 Sorted by residual: bond pdb=" CZ ARG C 77 " pdb=" NH2 ARG C 77 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" CZ ARG F 35 " pdb=" NH2 ARG F 35 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.05e+00 bond pdb=" CZ ARG E 132 " pdb=" NH2 ARG E 132 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.23e+00 bond pdb=" CZ ARG D 92 " pdb=" NH2 ARG D 92 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.11e+00 bond pdb=" CZ ARG C 77 " pdb=" NH1 ARG C 77 " ideal model delta sigma weight residual 1.323 1.283 0.040 1.40e-02 5.10e+03 8.08e+00 ... (remaining 11166 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.24: 1066 105.24 - 112.08: 6157 112.08 - 118.93: 2849 118.93 - 125.77: 5255 125.77 - 132.61: 842 Bond angle restraints: 16169 Sorted by residual: angle pdb=" CA CYS E 83 " pdb=" C CYS E 83 " pdb=" N PHE E 84 " ideal model delta sigma weight residual 115.55 122.08 -6.53 1.33e+00 5.65e-01 2.41e+01 angle pdb=" C LEU A 61 " pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 123.14 129.14 -6.00 1.31e+00 5.83e-01 2.10e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.58 126.32 -5.74 1.32e+00 5.74e-01 1.89e+01 angle pdb=" C ASN C 73 " pdb=" N LYS C 74 " pdb=" CA LYS C 74 " ideal model delta sigma weight residual 122.07 128.08 -6.01 1.43e+00 4.89e-01 1.76e+01 angle pdb=" C ARG A 116 " pdb=" N VAL A 117 " pdb=" CA VAL A 117 " ideal model delta sigma weight residual 121.84 126.31 -4.47 1.13e+00 7.83e-01 1.56e+01 ... (remaining 16164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 4839 35.82 - 71.65: 1170 71.65 - 107.47: 9 107.47 - 143.29: 3 143.29 - 179.12: 3 Dihedral angle restraints: 6024 sinusoidal: 4069 harmonic: 1955 Sorted by residual: dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N CYS A 83 " pdb=" CA CYS A 83 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta harmonic sigma weight residual 122.80 133.49 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" CA THR A 80 " pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1755 0.082 - 0.164: 85 0.164 - 0.245: 6 0.245 - 0.327: 2 0.327 - 0.409: 2 Chirality restraints: 1850 Sorted by residual: chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA LYS E 122 " pdb=" N LYS E 122 " pdb=" C LYS E 122 " pdb=" CB LYS E 122 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG H 33 " pdb=" N ARG H 33 " pdb=" C ARG H 33 " pdb=" CB ARG H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1847 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 78 " 0.044 2.00e-02 2.50e+03 2.81e-02 1.38e+01 pdb=" CG PHE A 78 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 78 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 78 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 78 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 78 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 100 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE B 100 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE B 100 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 92 " -0.281 9.50e-02 1.11e+02 1.26e-01 1.02e+01 pdb=" NE ARG H 92 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 92 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 92 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 92 " -0.014 2.00e-02 2.50e+03 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1387 2.76 - 3.29: 9078 3.29 - 3.83: 20471 3.83 - 4.36: 23963 4.36 - 4.90: 34740 Nonbonded interactions: 89639 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.390 2.520 nonbonded pdb=" NH1 ARG C 88 " pdb=" OD1 ASN C 94 " model vdw 2.417 2.520 ... (remaining 89634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 61 through 132) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 106) selection = (chain 'G' and resid 16 through 106) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.370 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.005 0.075 11171 Z= 0.327 Angle : 0.748 8.955 16169 Z= 0.463 Chirality : 0.044 0.409 1850 Planarity : 0.008 0.126 1168 Dihedral : 28.389 179.118 4766 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.29 % Cbeta Deviations : 0.16 % 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: 1.47 (0.32), residues: 661 helix: 1.84 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS H 82 PHE 0.044 0.004 PHE A 78 TYR 0.023 0.002 TYR F 88 ARG 0.011 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.729 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.3815 time to fit residues: 39.3344 Evaluate side-chains 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11171 Z= 0.326 Angle : 0.640 7.906 16169 Z= 0.373 Chirality : 0.038 0.131 1850 Planarity : 0.005 0.064 1168 Dihedral : 31.547 178.430 3477 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.54 % Allowed : 6.79 % Favored : 92.68 % 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: 1.40 (0.32), residues: 661 helix: 1.80 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 49 PHE 0.031 0.002 PHE G 25 TYR 0.018 0.002 TYR F 88 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.810 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.4057 time to fit residues: 36.1156 Evaluate side-chains 67 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0927 time to fit residues: 1.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7504 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11171 Z= 0.204 Angle : 0.556 7.225 16169 Z= 0.332 Chirality : 0.034 0.125 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.322 178.838 3477 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.36 % Allowed : 9.82 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.32), residues: 661 helix: 2.33 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.86 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.017 0.002 PHE G 25 TYR 0.015 0.001 TYR F 88 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.832 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.3809 time to fit residues: 33.6059 Evaluate side-chains 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0979 time to fit residues: 1.1947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11171 Z= 0.285 Angle : 0.604 7.534 16169 Z= 0.355 Chirality : 0.037 0.131 1850 Planarity : 0.005 0.067 1168 Dihedral : 31.487 179.356 3477 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.71 % Allowed : 11.61 % Favored : 87.68 % 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: 1.86 (0.32), residues: 661 helix: 2.12 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 49 PHE 0.026 0.002 PHE G 25 TYR 0.018 0.002 TYR F 88 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.803 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.3484 time to fit residues: 28.6776 Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0928 time to fit residues: 1.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11171 Z= 0.220 Angle : 0.561 7.510 16169 Z= 0.334 Chirality : 0.034 0.128 1850 Planarity : 0.004 0.068 1168 Dihedral : 31.360 179.989 3477 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.89 % Allowed : 12.68 % Favored : 86.43 % 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: 2.21 (0.33), residues: 661 helix: 2.38 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE G 25 TYR 0.017 0.001 TYR F 88 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.813 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.3717 time to fit residues: 33.6398 Evaluate side-chains 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0944 time to fit residues: 1.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11171 Z= 0.189 Angle : 0.548 7.630 16169 Z= 0.328 Chirality : 0.033 0.125 1850 Planarity : 0.004 0.066 1168 Dihedral : 31.285 179.727 3477 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.36 % Allowed : 13.39 % Favored : 86.25 % 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: 2.47 (0.33), residues: 661 helix: 2.58 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE G 25 TYR 0.020 0.001 TYR F 88 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.883 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.3732 time to fit residues: 29.1814 Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0963 time to fit residues: 1.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7479 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11171 Z= 0.170 Angle : 0.533 7.699 16169 Z= 0.321 Chirality : 0.033 0.124 1850 Planarity : 0.004 0.064 1168 Dihedral : 31.177 179.153 3477 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 14.29 % Favored : 85.54 % 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: 2.76 (0.33), residues: 661 helix: 2.81 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.017 0.001 TYR F 88 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.758 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.3689 time to fit residues: 30.8300 Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11171 Z= 0.262 Angle : 0.583 7.452 16169 Z= 0.343 Chirality : 0.035 0.131 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.300 179.797 3477 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.36 % Allowed : 15.00 % Favored : 84.64 % 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: 2.34 (0.32), residues: 661 helix: 2.49 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.82 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.016 0.002 PHE G 25 TYR 0.019 0.002 TYR F 88 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.774 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.3919 time to fit residues: 30.6890 Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0887 time to fit residues: 1.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7513 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11171 Z= 0.204 Angle : 0.557 7.702 16169 Z= 0.332 Chirality : 0.034 0.125 1850 Planarity : 0.004 0.064 1168 Dihedral : 31.293 178.860 3477 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % 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: 2.44 (0.32), residues: 661 helix: 2.58 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE G 25 TYR 0.018 0.001 TYR F 88 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.815 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3671 time to fit residues: 29.6111 Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11171 Z= 0.219 Angle : 0.560 7.651 16169 Z= 0.333 Chirality : 0.034 0.127 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.274 178.560 3477 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % 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: 2.43 (0.32), residues: 661 helix: 2.57 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.012 0.001 PHE G 25 TYR 0.018 0.001 TYR F 88 ARG 0.002 0.000 ARG F 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.891 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3636 time to fit residues: 29.0255 Evaluate side-chains 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122802 restraints weight = 12826.347| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.11 r_work: 0.3091 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11171 Z= 0.178 Angle : 0.546 7.904 16169 Z= 0.327 Chirality : 0.034 0.123 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.265 178.178 3477 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 15.18 % Favored : 84.64 % 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: 2.64 (0.32), residues: 661 helix: 2.73 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE D 65 TYR 0.016 0.001 TYR F 88 ARG 0.002 0.000 ARG F 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.92 seconds wall clock time: 31 minutes 22.16 seconds (1882.16 seconds total)