Starting phenix.real_space_refine on Wed Sep 25 09:09:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/09_2024/7vbm_31882.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/09_2024/7vbm_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_31882/09_2024/7vbm_31882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/09_2024/7vbm_31882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/09_2024/7vbm_31882.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/09_2024/7vbm_31882.cif" } 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. Time to flip 7 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: 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: 6.28, per 1000 atoms: 0.60 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 - 3.00 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: 2.65 Conformation dependent library (CDL) restraints added in 660.2 milliseconds 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: 4.75 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: 3.89 Time building geometry restraints manager: 3.12 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: 0.00 - 1.79: 15537 1.79 - 3.58: 548 3.58 - 5.37: 64 5.37 - 7.16: 17 7.16 - 8.96: 3 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 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.390 3.120 nonbonded pdb=" NH1 ARG C 88 " pdb=" OD1 ASN C 94 " model vdw 2.417 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.020 ------------------------------------------------------------------------------- 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 : 0.750 Fit side-chains REVERT: C 61 GLU cc_start: 0.8119 (tp30) cc_final: 0.7777 (tp30) REVERT: E 79 LYS cc_start: 0.7036 (tppt) cc_final: 0.6548 (tptt) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.3611 time to fit residues: 37.2292 Evaluate side-chains 70 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11171 Z= 0.262 Angle : 0.601 7.989 16169 Z= 0.355 Chirality : 0.036 0.126 1850 Planarity : 0.005 0.059 1168 Dihedral : 31.365 179.508 3477 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.36 % Allowed : 6.43 % Favored : 93.21 % 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: 1.75 (0.32), residues: 661 helix: 2.05 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 49 PHE 0.023 0.002 PHE G 25 TYR 0.016 0.002 TYR F 88 ARG 0.003 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 73 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.775 Fit side-chains REVERT: C 61 GLU cc_start: 0.8124 (tp30) cc_final: 0.7814 (tp30) REVERT: D 59 MET cc_start: 0.7766 (tpp) cc_final: 0.7297 (tpp) REVERT: F 93 GLN cc_start: 0.8113 (mp10) cc_final: 0.7650 (mp10) REVERT: H 33 ARG cc_start: 0.5557 (mtm180) cc_final: 0.5330 (mtm180) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.3701 time to fit residues: 33.9759 Evaluate side-chains 65 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 10.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7505 moved from start: 0.1002 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= 0.203 Angle : 0.557 7.318 16169 Z= 0.334 Chirality : 0.034 0.125 1850 Planarity : 0.004 0.063 1168 Dihedral : 31.260 178.880 3477 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % 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: 2.26 (0.32), residues: 661 helix: 2.42 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE G 25 TYR 0.014 0.001 TYR F 88 ARG 0.006 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 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.755 Fit side-chains REVERT: C 61 GLU cc_start: 0.8157 (tp30) cc_final: 0.7867 (tp30) REVERT: D 59 MET cc_start: 0.7682 (tpp) cc_final: 0.7218 (tpp) REVERT: D 76 GLU cc_start: 0.8190 (tp30) cc_final: 0.7990 (tp30) REVERT: F 93 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7675 (mp10) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.3751 time to fit residues: 30.8576 Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1134 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= 0.310 Angle : 0.622 7.975 16169 Z= 0.364 Chirality : 0.038 0.131 1850 Planarity : 0.005 0.066 1168 Dihedral : 31.522 179.658 3477 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.89 % Allowed : 10.89 % Favored : 88.21 % 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: 1.76 (0.32), residues: 661 helix: 2.09 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 49 PHE 0.029 0.002 PHE G 25 TYR 0.016 0.002 TYR F 88 ARG 0.003 0.000 ARG H 72 *********************** 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 67 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.753 Fit side-chains REVERT: C 61 GLU cc_start: 0.8182 (tp30) cc_final: 0.7901 (tp30) REVERT: D 59 MET cc_start: 0.7748 (tpp) cc_final: 0.7290 (tpp) REVERT: E 125 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: F 93 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7724 (mp10) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.3174 time to fit residues: 27.5232 Evaluate side-chains 67 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.1258 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= 0.210 Angle : 0.555 7.198 16169 Z= 0.332 Chirality : 0.034 0.125 1850 Planarity : 0.004 0.068 1168 Dihedral : 31.313 179.897 3477 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.07 % Allowed : 12.32 % Favored : 86.61 % 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: 2.25 (0.32), residues: 661 helix: 2.45 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE G 25 TYR 0.015 0.001 TYR F 88 ARG 0.003 0.000 ARG B 23 *********************** 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 73 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.801 Fit side-chains REVERT: C 61 GLU cc_start: 0.8160 (tp30) cc_final: 0.7909 (tp30) REVERT: D 59 MET cc_start: 0.7710 (tpp) cc_final: 0.7506 (tpp) REVERT: E 125 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: F 93 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7672 (mp10) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.3400 time to fit residues: 30.6125 Evaluate side-chains 70 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7478 moved from start: 0.1364 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= 0.159 Angle : 0.536 7.594 16169 Z= 0.323 Chirality : 0.033 0.120 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.266 179.971 3477 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.07 % Allowed : 12.86 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.70 (0.32), residues: 661 helix: 2.76 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.72 (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 D 65 TYR 0.017 0.001 TYR F 88 ARG 0.003 0.000 ARG B 39 *********************** 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 68 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.757 Fit side-chains REVERT: C 61 GLU cc_start: 0.8195 (tp30) cc_final: 0.7962 (tp30) REVERT: E 125 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: F 93 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7790 (mp10) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.3116 time to fit residues: 26.9369 Evaluate side-chains 65 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 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: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7494 moved from start: 0.1396 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= 0.193 Angle : 0.545 7.384 16169 Z= 0.327 Chirality : 0.033 0.124 1850 Planarity : 0.004 0.063 1168 Dihedral : 31.250 179.690 3477 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.25 % Allowed : 13.21 % 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: 2.71 (0.32), residues: 661 helix: 2.77 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.72 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.001 PHE G 25 TYR 0.014 0.001 TYR F 88 ARG 0.003 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 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.745 Fit side-chains REVERT: B 92 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7796 (ttp80) REVERT: C 61 GLU cc_start: 0.8157 (tp30) cc_final: 0.7914 (tp30) REVERT: D 46 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7799 (mmtm) REVERT: E 125 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: F 93 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7697 (mp10) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.3518 time to fit residues: 28.3563 Evaluate side-chains 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 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: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.1359 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= 0.271 Angle : 0.590 7.546 16169 Z= 0.348 Chirality : 0.036 0.131 1850 Planarity : 0.005 0.063 1168 Dihedral : 31.387 179.746 3477 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.61 % Allowed : 13.04 % Favored : 85.36 % 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: 2.32 (0.32), residues: 661 helix: 2.50 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 49 PHE 0.020 0.002 PHE G 25 TYR 0.017 0.002 TYR F 88 ARG 0.003 0.000 ARG H 72 *********************** 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 71 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.754 Fit side-chains REVERT: C 61 GLU cc_start: 0.8152 (tp30) cc_final: 0.7900 (tp30) REVERT: D 46 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7838 (mmtm) REVERT: D 47 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: E 125 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: F 93 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7695 (mp10) outliers start: 9 outliers final: 3 residues processed: 67 average time/residue: 0.3445 time to fit residues: 29.4709 Evaluate side-chains 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 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: 0.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7493 moved from start: 0.1501 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= 0.191 Angle : 0.542 7.545 16169 Z= 0.325 Chirality : 0.033 0.123 1850 Planarity : 0.004 0.063 1168 Dihedral : 31.240 178.073 3477 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.25 % Allowed : 13.57 % Favored : 85.18 % 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: 2.62 (0.32), residues: 661 helix: 2.73 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE G 25 TYR 0.017 0.001 TYR F 88 ARG 0.003 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 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.893 Fit side-chains REVERT: C 61 GLU cc_start: 0.8176 (tp30) cc_final: 0.7946 (tp30) REVERT: D 46 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7785 (mmtm) REVERT: E 125 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: F 93 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7692 (mp10) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 0.3262 time to fit residues: 27.6980 Evaluate side-chains 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN 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: 8.9990 chunk 70 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.1531 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= 0.159 Angle : 0.535 7.821 16169 Z= 0.322 Chirality : 0.033 0.125 1850 Planarity : 0.004 0.062 1168 Dihedral : 31.247 178.140 3477 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.25 % Allowed : 13.39 % Favored : 85.36 % 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: 2.86 (0.33), residues: 661 helix: 2.91 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.79 (0.41), 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 0.016 0.001 TYR F 88 ARG 0.002 0.000 ARG A 116 ********************** 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 68 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.706 Fit side-chains REVERT: C 61 GLU cc_start: 0.8173 (tp30) cc_final: 0.7946 (tp30) REVERT: D 46 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (mmtm) REVERT: E 125 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: F 93 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7767 (mp10) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.3190 time to fit residues: 27.2267 Evaluate side-chains 66 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124027 restraints weight = 12913.208| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.11 r_work: 0.3075 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1549 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= 0.175 Angle : 0.537 7.701 16169 Z= 0.322 Chirality : 0.033 0.123 1850 Planarity : 0.004 0.063 1168 Dihedral : 31.226 177.951 3477 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.07 % Allowed : 13.57 % Favored : 85.36 % 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: 2.83 (0.32), residues: 661 helix: 2.88 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.77 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE D 65 TYR 0.016 0.001 TYR F 88 ARG 0.002 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.48 seconds wall clock time: 34 minutes 25.46 seconds (2065.46 seconds total)