Starting phenix.real_space_refine on Sat Dec 9 12:34:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8n_24238/12_2023/7n8n_24238.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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 248 5.49 5 S 30 5.16 5 C 6180 2.51 5 N 2053 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1501 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain: "D" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2543 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2576 Classifications: {'DNA': 125} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 124} Time building chain proxies: 6.18, per 1000 atoms: 0.56 Number of scatterers: 11121 At special positions: 0 Unit cell: (86.265, 111.825, 116.085, 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 30 16.00 P 248 15.00 O 2610 8.00 N 2053 7.00 C 6180 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: 7.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 67.4% alpha, 0.5% beta 124 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.561A pdb=" N VAL A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.975A pdb=" N GLN A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 172 through 201 Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 81 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 4.885A pdb=" N GLU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 54 through 80 removed outlier: 3.701A pdb=" N ILE C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.562A pdb=" N VAL C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.976A pdb=" N GLN C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 172 through 201 Processing helix chain 'C' and resid 207 through 219 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 129 through 133 removed outlier: 4.171A pdb=" N SER D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 removed outlier: 4.884A pdb=" N GLU D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 205 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 388 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 7.47 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: 2475 1.33 - 1.45: 3579 1.45 - 1.57: 5210 1.57 - 1.69: 496 1.69 - 1.81: 52 Bond restraints: 11812 Sorted by residual: bond pdb=" CZ ARG B 157 " pdb=" NH2 ARG B 157 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.01e+00 bond pdb=" CZ ARG D 157 " pdb=" NH2 ARG D 157 " ideal model delta sigma weight residual 1.330 1.308 0.022 1.30e-02 5.92e+03 2.98e+00 bond pdb=" CA VAL A 56 " pdb=" CB VAL A 56 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.77e+00 bond pdb=" CA VAL C 56 " pdb=" CB VAL C 56 " ideal model delta sigma weight residual 1.539 1.547 -0.008 5.40e-03 3.43e+04 2.30e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 11807 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.25: 931 104.25 - 111.35: 6057 111.35 - 118.45: 3564 118.45 - 125.55: 5631 125.55 - 132.65: 814 Bond angle restraints: 16997 Sorted by residual: angle pdb=" CB MET C 157 " pdb=" CG MET C 157 " pdb=" SD MET C 157 " ideal model delta sigma weight residual 112.70 102.55 10.15 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 102.57 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CA LEU B 166 " pdb=" CB LEU B 166 " pdb=" CG LEU B 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" CA LEU D 166 " pdb=" CB LEU D 166 " pdb=" CG LEU D 166 " ideal model delta sigma weight residual 116.30 105.03 11.27 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C4 DT I -64 " pdb=" C5 DT I -64 " pdb=" C7 DT I -64 " ideal model delta sigma weight residual 122.40 117.59 4.81 1.50e+00 4.44e-01 1.03e+01 ... (remaining 16992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5236 34.91 - 69.81: 1210 69.81 - 104.72: 17 104.72 - 139.63: 2 139.63 - 174.54: 3 Dihedral angle restraints: 6468 sinusoidal: 4198 harmonic: 2270 Sorted by residual: dihedral pdb=" CA SER C 131 " pdb=" C SER C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta harmonic sigma weight residual -180.00 -63.39 -116.61 0 5.00e+00 4.00e-02 5.44e+02 dihedral pdb=" CA SER A 131 " pdb=" C SER A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual -180.00 -63.45 -116.55 0 5.00e+00 4.00e-02 5.43e+02 dihedral pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" N GLY C 113 " pdb=" CA GLY C 113 " ideal model delta harmonic sigma weight residual -180.00 -99.23 -80.77 0 5.00e+00 4.00e-02 2.61e+02 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1311 0.036 - 0.072: 474 0.072 - 0.108: 133 0.108 - 0.143: 39 0.143 - 0.179: 7 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CG LEU C 41 " pdb=" CB LEU C 41 " pdb=" CD1 LEU C 41 " pdb=" CD2 LEU C 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1961 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 135 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C LYS B 135 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS B 135 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 136 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 135 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LYS D 135 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS D 135 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 136 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 65 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" CG ASN D 65 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN D 65 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN D 65 " -0.016 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 246 2.61 - 3.18: 10949 3.18 - 3.75: 22515 3.75 - 4.33: 27845 4.33 - 4.90: 37785 Nonbonded interactions: 99340 Sorted by model distance: nonbonded pdb=" O GLU A 132 " pdb=" OG SER A 135 " model vdw 2.035 2.440 nonbonded pdb=" O GLU C 132 " pdb=" OG SER C 135 " model vdw 2.036 2.440 nonbonded pdb=" OG SER A 185 " pdb=" O GLY D 219 " model vdw 2.101 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 38 " model vdw 2.103 2.440 nonbonded pdb=" O LYS C 35 " pdb=" OG1 THR C 38 " model vdw 2.104 2.440 ... (remaining 99335 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 39.290 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.006 0.045 11812 Z= 0.360 Angle : 0.849 11.271 16997 Z= 0.504 Chirality : 0.042 0.179 1964 Planarity : 0.006 0.054 1276 Dihedral : 27.929 174.537 5000 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.71 (0.28), residues: 790 helix: -0.13 (0.22), residues: 484 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS C 219 PHE 0.024 0.004 PHE C 154 TYR 0.020 0.002 TYR D 121 ARG 0.007 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2179 time to fit residues: 56.4182 Evaluate side-chains 110 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11812 Z= 0.285 Angle : 0.746 11.175 16997 Z= 0.429 Chirality : 0.042 0.268 1964 Planarity : 0.006 0.065 1276 Dihedral : 31.036 174.452 3544 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.10 % Favored : 91.65 % Rotamer: Outliers : 4.95 % Allowed : 12.07 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.29 (0.28), residues: 790 helix: 0.10 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS C 67 PHE 0.017 0.002 PHE A 61 TYR 0.025 0.003 TYR B 172 ARG 0.006 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 148 average time/residue: 0.2085 time to fit residues: 45.0181 Evaluate side-chains 131 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1023 time to fit residues: 4.6925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 65 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11812 Z= 0.255 Angle : 0.697 6.276 16997 Z= 0.404 Chirality : 0.040 0.164 1964 Planarity : 0.006 0.070 1276 Dihedral : 30.902 175.710 3544 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 2.32 % Allowed : 15.63 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.06 (0.28), residues: 790 helix: 0.29 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.57 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 67 PHE 0.017 0.002 PHE D 173 TYR 0.025 0.002 TYR B 121 ARG 0.005 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 0.2116 time to fit residues: 40.7765 Evaluate side-chains 113 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1054 time to fit residues: 1.8350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11812 Z= 0.273 Angle : 0.697 7.207 16997 Z= 0.405 Chirality : 0.039 0.194 1964 Planarity : 0.006 0.074 1276 Dihedral : 30.946 176.643 3544 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.85 % Favored : 91.90 % Rotamer: Outliers : 2.01 % Allowed : 20.28 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.02 (0.29), residues: 790 helix: 0.29 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.47 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 167 PHE 0.040 0.003 PHE A 154 TYR 0.026 0.002 TYR B 121 ARG 0.004 0.001 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.1980 time to fit residues: 35.0261 Evaluate side-chains 111 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1021 time to fit residues: 2.6039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11812 Z= 0.220 Angle : 0.671 8.218 16997 Z= 0.389 Chirality : 0.038 0.161 1964 Planarity : 0.005 0.073 1276 Dihedral : 30.914 177.237 3544 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 1.08 % Allowed : 23.22 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.29), residues: 790 helix: 0.41 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 167 PHE 0.044 0.003 PHE C 116 TYR 0.026 0.002 TYR B 121 ARG 0.004 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 122 average time/residue: 0.2113 time to fit residues: 37.6062 Evaluate side-chains 110 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1151 time to fit residues: 1.8079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11812 Z= 0.217 Angle : 0.666 8.255 16997 Z= 0.385 Chirality : 0.037 0.160 1964 Planarity : 0.005 0.071 1276 Dihedral : 30.897 177.345 3544 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.58 % Favored : 93.16 % Rotamer: Outliers : 1.86 % Allowed : 25.70 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.29), residues: 790 helix: 0.47 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.34 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 67 PHE 0.042 0.003 PHE C 116 TYR 0.024 0.002 TYR B 121 ARG 0.012 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 122 average time/residue: 0.2129 time to fit residues: 37.7760 Evaluate side-chains 109 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1089 time to fit residues: 1.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11812 Z= 0.203 Angle : 0.669 8.626 16997 Z= 0.384 Chirality : 0.038 0.333 1964 Planarity : 0.005 0.070 1276 Dihedral : 30.872 177.469 3544 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.80 % Rotamer: Outliers : 1.70 % Allowed : 26.16 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.29), residues: 790 helix: 0.64 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.33 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 170 PHE 0.024 0.002 PHE C 154 TYR 0.027 0.002 TYR B 121 ARG 0.007 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 0.2313 time to fit residues: 39.2274 Evaluate side-chains 115 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1702 time to fit residues: 2.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 9 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 3.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11812 Z= 0.329 Angle : 0.726 10.553 16997 Z= 0.418 Chirality : 0.041 0.252 1964 Planarity : 0.006 0.071 1276 Dihedral : 31.068 179.247 3544 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.73 % Favored : 91.01 % Rotamer: Outliers : 1.08 % Allowed : 27.55 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.29), residues: 790 helix: 0.51 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 63 PHE 0.031 0.003 PHE C 116 TYR 0.030 0.002 TYR B 121 ARG 0.010 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 105 average time/residue: 0.2215 time to fit residues: 33.6210 Evaluate side-chains 103 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.805 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1056 time to fit residues: 2.1998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 11812 Z= 0.470 Angle : 0.852 10.459 16997 Z= 0.490 Chirality : 0.046 0.358 1964 Planarity : 0.008 0.083 1276 Dihedral : 31.656 175.971 3544 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 37.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.25 % Favored : 89.49 % Rotamer: Outliers : 1.08 % Allowed : 28.17 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.56 (0.27), residues: 790 helix: -0.12 (0.21), residues: 504 sheet: None (None), residues: 0 loop : -2.70 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 167 PHE 0.030 0.004 PHE C 154 TYR 0.035 0.003 TYR B 121 ARG 0.026 0.002 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.2045 time to fit residues: 31.4473 Evaluate side-chains 101 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1053 time to fit residues: 1.8185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 HIS ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11812 Z= 0.334 Angle : 0.772 9.315 16997 Z= 0.443 Chirality : 0.042 0.236 1964 Planarity : 0.007 0.099 1276 Dihedral : 31.706 175.250 3544 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.48 % Favored : 91.27 % Rotamer: Outliers : 0.46 % Allowed : 29.10 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.34 (0.28), residues: 790 helix: 0.10 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.74 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 167 PHE 0.027 0.003 PHE C 116 TYR 0.030 0.003 TYR B 121 ARG 0.022 0.001 ARG C 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 0.2059 time to fit residues: 31.6749 Evaluate side-chains 101 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1117 time to fit residues: 1.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.059538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043750 restraints weight = 70867.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045337 restraints weight = 42825.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046353 restraints weight = 30486.439| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11812 Z= 0.253 Angle : 0.723 9.411 16997 Z= 0.414 Chirality : 0.040 0.224 1964 Planarity : 0.006 0.071 1276 Dihedral : 31.546 174.864 3544 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.72 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 29.88 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.10 (0.29), residues: 790 helix: 0.31 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 167 PHE 0.026 0.003 PHE C 116 TYR 0.025 0.002 TYR B 121 ARG 0.005 0.001 ARG B 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.93 seconds wall clock time: 39 minutes 6.43 seconds (2346.43 seconds total)