Starting phenix.real_space_refine on Thu Dec 7 19:02:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/12_2023/7zj2_14739.pdb" } resolution = 3.32 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= 0.032 sd= 0.409 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2292 2.51 5 N 696 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3792 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "D" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "E" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "F" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "G" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "H" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "I" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "J" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "K" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "L" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Time building chain proxies: 2.23, per 1000 atoms: 0.59 Number of scatterers: 3792 At special positions: 0 Unit cell: (73.84, 75.92, 47.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 792 8.00 N 696 7.00 C 2292 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: 1.42 Conformation dependent library (CDL) restraints added in 727.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN A 269 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN C 272 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 271 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN C 269 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN E 272 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER C 271 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN E 269 " --> pdb=" O SER G 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN G 272 " --> pdb=" O GLN E 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 271 " --> pdb=" O ASN G 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN G 269 " --> pdb=" O SER I 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN I 272 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER G 271 " --> pdb=" O ASN I 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN I 269 " --> pdb=" O SER K 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN K 272 " --> pdb=" O GLN I 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 271 " --> pdb=" O ASN K 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN B 269 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN D 272 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 271 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN D 269 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN F 272 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER D 271 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN F 269 " --> pdb=" O SER H 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN H 272 " --> pdb=" O GLN F 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER F 271 " --> pdb=" O ASN H 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN H 269 " --> pdb=" O SER J 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN J 272 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER H 271 " --> pdb=" O ASN J 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN J 269 " --> pdb=" O SER L 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN L 272 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER J 271 " --> pdb=" O ASN L 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.05 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 672 1.31 - 1.43: 1368 1.43 - 1.56: 1836 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 3900 Sorted by residual: bond pdb=" C PRO L 288 " pdb=" O PRO L 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO I 288 " pdb=" O PRO I 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO A 288 " pdb=" O PRO A 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO E 288 " pdb=" O PRO E 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 bond pdb=" C PRO F 288 " pdb=" O PRO F 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 100.21 - 105.51: 180 105.51 - 110.81: 555 110.81 - 116.11: 1034 116.11 - 121.41: 2124 121.41 - 126.72: 1291 Bond angle restraints: 5184 Sorted by residual: angle pdb=" CA GLY A 291 " pdb=" C GLY A 291 " pdb=" O GLY A 291 " ideal model delta sigma weight residual 122.23 117.52 4.71 6.90e-01 2.10e+00 4.67e+01 angle pdb=" CA GLY I 291 " pdb=" C GLY I 291 " pdb=" O GLY I 291 " ideal model delta sigma weight residual 122.23 117.54 4.69 6.90e-01 2.10e+00 4.62e+01 angle pdb=" CA GLY C 291 " pdb=" C GLY C 291 " pdb=" O GLY C 291 " ideal model delta sigma weight residual 122.23 117.55 4.68 6.90e-01 2.10e+00 4.60e+01 angle pdb=" CA GLY G 291 " pdb=" C GLY G 291 " pdb=" O GLY G 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 angle pdb=" CA GLY K 291 " pdb=" C GLY K 291 " pdb=" O GLY K 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 ... (remaining 5179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 1779 14.96 - 29.91: 177 29.91 - 44.86: 12 44.86 - 59.82: 24 59.82 - 74.77: 24 Dihedral angle restraints: 2016 sinusoidal: 744 harmonic: 1272 Sorted by residual: dihedral pdb=" CA ASN J 268 " pdb=" CB ASN J 268 " pdb=" CG ASN J 268 " pdb=" OD1 ASN J 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.75 70.75 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN F 268 " pdb=" CB ASN F 268 " pdb=" CG ASN F 268 " pdb=" OD1 ASN F 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN L 268 " pdb=" CB ASN L 268 " pdb=" CG ASN L 268 " pdb=" OD1 ASN L 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 120 0.034 - 0.068: 96 0.068 - 0.102: 48 0.102 - 0.136: 36 0.136 - 0.170: 48 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA TYR F 260 " pdb=" N TYR F 260 " pdb=" C TYR F 260 " pdb=" CB TYR F 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR J 260 " pdb=" N TYR J 260 " pdb=" C TYR J 260 " pdb=" CB TYR J 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA TYR H 260 " pdb=" N TYR H 260 " pdb=" C TYR H 260 " pdb=" CB TYR H 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 345 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 270 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER J 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER J 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER J 271 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 270 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER E 270 " 0.058 2.00e-02 2.50e+03 pdb=" O SER E 270 " -0.022 2.00e-02 2.50e+03 pdb=" N SER E 271 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 270 " 0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER L 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER L 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER L 271 " 0.020 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2390 3.02 - 3.49: 3846 3.49 - 3.96: 6869 3.96 - 4.43: 7785 4.43 - 4.90: 15100 Nonbonded interactions: 35990 Sorted by model distance: nonbonded pdb=" N SER F 286 " pdb=" O SER F 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER L 286 " pdb=" O SER L 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER D 286 " pdb=" O SER D 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER B 286 " pdb=" O SER B 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER H 286 " pdb=" O SER H 286 " model vdw 2.548 2.496 ... (remaining 35985 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 3.540 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.014 0.054 3900 Z= 1.050 Angle : 2.210 8.127 5184 Z= 1.661 Chirality : 0.082 0.170 348 Planarity : 0.011 0.034 780 Dihedral : 15.288 74.770 1320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE F 273 TYR 0.029 0.004 TYR D 260 ARG 0.003 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1663 time to fit residues: 48.7149 Evaluate side-chains 180 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3900 Z= 0.145 Angle : 0.544 4.193 5184 Z= 0.313 Chirality : 0.030 0.093 348 Planarity : 0.004 0.022 780 Dihedral : 4.417 10.690 588 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.75 % Allowed : 25.00 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.25), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.19), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE C 263 TYR 0.020 0.002 TYR G 260 ARG 0.002 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 0.382 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 164 average time/residue: 0.1293 time to fit residues: 26.7860 Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0394 time to fit residues: 1.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3900 Z= 0.227 Angle : 0.544 4.278 5184 Z= 0.311 Chirality : 0.032 0.115 348 Planarity : 0.004 0.021 780 Dihedral : 4.460 10.325 588 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 5.17 % Allowed : 24.71 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.044 0.003 PHE L 263 TYR 0.020 0.002 TYR H 266 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.415 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 155 average time/residue: 0.1268 time to fit residues: 24.9302 Evaluate side-chains 147 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0472 time to fit residues: 1.2069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN C 261 ASN J 261 ASN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3900 Z= 0.111 Angle : 0.472 3.811 5184 Z= 0.274 Chirality : 0.031 0.098 348 Planarity : 0.003 0.015 780 Dihedral : 3.793 9.975 588 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.02 % Allowed : 27.01 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE D 281 TYR 0.020 0.002 TYR H 266 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.435 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 148 average time/residue: 0.1243 time to fit residues: 23.5343 Evaluate side-chains 138 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0449 time to fit residues: 1.4119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN D 261 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3900 Z= 0.138 Angle : 0.474 3.797 5184 Z= 0.273 Chirality : 0.030 0.097 348 Planarity : 0.003 0.017 780 Dihedral : 3.731 10.593 588 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.17 % Allowed : 24.43 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.003 PHE K 263 TYR 0.020 0.002 TYR H 266 ARG 0.003 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.427 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 135 average time/residue: 0.1246 time to fit residues: 21.4779 Evaluate side-chains 134 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0455 time to fit residues: 1.6329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 261 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 3900 Z= 0.349 Angle : 0.582 3.825 5184 Z= 0.334 Chirality : 0.032 0.089 348 Planarity : 0.004 0.024 780 Dihedral : 4.681 13.257 588 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.17 % Allowed : 24.14 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.004 PHE I 273 TYR 0.029 0.003 TYR E 266 ARG 0.002 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.385 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 136 average time/residue: 0.1333 time to fit residues: 22.8664 Evaluate side-chains 127 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0412 time to fit residues: 0.9532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 261 ASN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3900 Z= 0.149 Angle : 0.485 4.785 5184 Z= 0.275 Chirality : 0.030 0.099 348 Planarity : 0.003 0.020 780 Dihedral : 3.827 11.654 588 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.44 % Allowed : 26.72 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHE F 281 TYR 0.018 0.002 TYR H 266 ARG 0.002 0.001 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.444 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 136 average time/residue: 0.1292 time to fit residues: 22.3639 Evaluate side-chains 126 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0493 time to fit residues: 0.8336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 3900 Z= 0.315 Angle : 0.577 8.726 5184 Z= 0.323 Chirality : 0.031 0.092 348 Planarity : 0.004 0.025 780 Dihedral : 4.440 13.717 588 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.59 % Allowed : 28.45 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.003 PHE G 263 TYR 0.021 0.002 TYR C 260 ARG 0.002 0.000 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.359 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 122 average time/residue: 0.1302 time to fit residues: 20.1278 Evaluate side-chains 122 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0413 time to fit residues: 1.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3900 Z= 0.151 Angle : 0.508 8.242 5184 Z= 0.282 Chirality : 0.031 0.097 348 Planarity : 0.003 0.023 780 Dihedral : 3.795 13.925 588 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.86 % Allowed : 27.59 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.002 PHE G 263 TYR 0.028 0.002 TYR E 266 ARG 0.003 0.001 ARG H 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.394 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 119 average time/residue: 0.1319 time to fit residues: 20.0629 Evaluate side-chains 115 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0451 time to fit residues: 0.7326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3900 Z= 0.237 Angle : 0.540 4.264 5184 Z= 0.307 Chirality : 0.031 0.096 348 Planarity : 0.003 0.023 780 Dihedral : 4.072 12.415 588 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.86 % Allowed : 29.31 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE G 263 TYR 0.036 0.002 TYR G 266 ARG 0.002 0.001 ARG E 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.412 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 117 average time/residue: 0.1315 time to fit residues: 19.8353 Evaluate side-chains 113 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0520 time to fit residues: 0.6167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 265 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 = 0.4463 r_free = 0.4463 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.130943 restraints weight = 7045.603| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.06 r_work: 0.4228 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3900 Z= 0.234 Angle : 0.545 5.676 5184 Z= 0.309 Chirality : 0.032 0.103 348 Planarity : 0.003 0.024 780 Dihedral : 4.059 12.996 588 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.86 % Allowed : 31.03 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.002 PHE G 263 TYR 0.041 0.002 TYR G 266 ARG 0.002 0.000 ARG L 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.68 seconds wall clock time: 25 minutes 52.30 seconds (1552.30 seconds total)