Starting phenix.real_space_refine (version: dev) on Fri May 13 06:15:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/05_2022/7vbm_31882.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/05_2022/7vbm_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_31882/05_2022/7vbm_31882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/05_2022/7vbm_31882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/05_2022/7vbm_31882.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbm_31882/05_2022/7vbm_31882.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4597/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: 6.15, per 1000 atoms: 0.59 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: 5.18 Conformation dependent library (CDL) restraints added in 877.4 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: 4.47 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: 4.04 Time building geometry restraints manager: 5.51 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: 4646 35.82 - 71.65: 1159 71.65 - 107.47: 9 107.47 - 143.29: 3 143.29 - 179.12: 3 Dihedral angle restraints: 5820 sinusoidal: 3865 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 5817 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 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. 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.610 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.100 Process input model: 34.970 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 28.601 179.118 4562 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 % 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 *********************** 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 : 0.864 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.3451 time to fit residues: 36.1401 Evaluate side-chains 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9443 ------------------------------------------------------------------------------- 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: 7.9990 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: 0.9990 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: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.0891 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= 0.310 Angle : 0.628 8.233 16169 Z= 0.368 Chirality : 0.038 0.130 1850 Planarity : 0.005 0.062 1168 Dihedral : 32.014 178.783 3273 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.54 % 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: 1.49 (0.32), residues: 661 helix: 1.86 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 157 *********************** 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: 3 poor density : 70 time to evaluate : 0.878 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.3607 time to fit residues: 33.1149 Evaluate side-chains 67 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0861 time to fit residues: 1.2785 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 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: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.1034 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= 0.208 Angle : 0.556 7.264 16169 Z= 0.332 Chirality : 0.034 0.127 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.850 178.935 3273 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 0.36 % 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: 2.14 (0.32), residues: 661 helix: 2.34 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.85 (0.40), residues: 156 *********************** 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 69 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.898 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.3642 time to fit residues: 31.8998 Evaluate side-chains 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0960 time to fit residues: 1.1790 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7877 moved from start: 0.1200 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= 0.304 Angle : 0.618 7.822 16169 Z= 0.362 Chirality : 0.037 0.131 1850 Planarity : 0.005 0.067 1168 Dihedral : 32.088 179.918 3273 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.54 % 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: 1.74 (0.32), residues: 661 helix: 2.04 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 156 *********************** 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 62 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.884 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.3299 time to fit residues: 26.6735 Evaluate side-chains 60 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0948 time to fit residues: 1.1645 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.1244 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= 0.243 Angle : 0.576 7.527 16169 Z= 0.341 Chirality : 0.035 0.135 1850 Planarity : 0.004 0.070 1168 Dihedral : 31.936 179.799 3273 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.89 % 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: 1.99 (0.32), residues: 661 helix: 2.24 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 156 *********************** 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 68 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.833 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.3241 time to fit residues: 27.4462 Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0904 time to fit residues: 1.6501 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.1274 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= 0.260 Angle : 0.586 7.620 16169 Z= 0.346 Chirality : 0.036 0.128 1850 Planarity : 0.005 0.068 1168 Dihedral : 31.942 179.312 3273 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.71 % 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: 1.93 (0.32), residues: 661 helix: 2.20 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 156 *********************** 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 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.814 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.3638 time to fit residues: 28.0945 Evaluate side-chains 58 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5763 time to fit residues: 1.6497 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.1540 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 : 0.523 7.322 16169 Z= 0.316 Chirality : 0.032 0.122 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.664 178.449 3273 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.18 % 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: 2.69 (0.33), residues: 661 helix: 2.77 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 156 *********************** 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 71 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.913 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3328 time to fit residues: 29.9574 Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8781 ------------------------------------------------------------------------------- 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: 0.0980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 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: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.1514 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= 0.205 Angle : 0.547 7.552 16169 Z= 0.326 Chirality : 0.033 0.124 1850 Planarity : 0.004 0.066 1168 Dihedral : 31.696 178.604 3273 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % 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: 2.61 (0.33), residues: 661 helix: 2.72 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 156 *********************** 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 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.769 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3407 time to fit residues: 27.2828 Evaluate side-chains 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0273 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 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: 0.9980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.1523 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= 0.192 Angle : 0.543 7.474 16169 Z= 0.324 Chirality : 0.033 0.125 1850 Planarity : 0.004 0.066 1168 Dihedral : 31.698 178.488 3273 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.36 % 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: 2.64 (0.33), residues: 661 helix: 2.75 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.87 (0.41), residues: 156 *********************** 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: 2 poor density : 61 time to evaluate : 0.750 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.3394 time to fit residues: 26.8024 Evaluate side-chains 63 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1025 time to fit residues: 1.4241 ------------------------------------------------------------------------------- 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: 0.2980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.1528 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= 0.187 Angle : 0.541 7.505 16169 Z= 0.323 Chirality : 0.033 0.123 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.698 178.357 3273 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % 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: 2.66 (0.33), residues: 661 helix: 2.77 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 156 ********************** 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 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3315 time to fit residues: 26.2912 Evaluate side-chains 61 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9778 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.170512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119695 restraints weight = 12836.246| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.04 r_work: 0.3268 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1539 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= 0.177 Angle : 0.537 7.491 16169 Z= 0.322 Chirality : 0.033 0.123 1850 Planarity : 0.004 0.065 1168 Dihedral : 31.697 178.177 3273 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % 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: 2.72 (0.33), residues: 661 helix: 2.81 (0.23), residues: 505 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 156 =============================================================================== Job complete usr+sys time: 1399.14 seconds wall clock time: 26 minutes 28.09 seconds (1588.09 seconds total)