Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/03_2024/8olg_16957.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.001 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 5 5.16 5 C 945 2.51 5 N 270 2.21 5 O 270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1490 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "B" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "D" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "E" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Time building chain proxies: 1.09, per 1000 atoms: 0.73 Number of scatterers: 1490 At special positions: 0 Unit cell: (53.328, 57.368, 45.248, 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 5 16.00 O 270 8.00 N 270 7.00 C 945 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: 0.53 Conformation dependent library (CDL) restraints added in 221.6 milliseconds 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.132A pdb=" N ALA A 2 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 2 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 2 " --> pdb=" O GLU D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 27 removed outlier: 6.841A pdb=" N VAL B 24 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY A 25 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER B 26 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C 27 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL C 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN D 27 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N SER C 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE D 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN E 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN D 22 " --> pdb=" O ASN E 23 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLY E 25 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL D 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN E 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N SER D 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 35 removed outlier: 5.916A pdb=" N LEU A 34 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU B 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU C 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 11 hydrogen bonds defined for protein. 33 hydrogen bond angles 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: 0.31 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 510 1.34 - 1.46: 350 1.46 - 1.57: 650 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 1520 Sorted by residual: bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N ASP A 1 " pdb=" CA ASP A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 1515 not shown) Histogram of bond angle deviations from ideal: 100.92 - 107.02: 20 107.02 - 113.12: 802 113.12 - 119.22: 384 119.22 - 125.32: 814 125.32 - 131.42: 15 Bond angle restraints: 2035 Sorted by residual: angle pdb=" N HIS C 13 " pdb=" CA HIS C 13 " pdb=" C HIS C 13 " ideal model delta sigma weight residual 108.90 110.94 -2.04 1.63e+00 3.76e-01 1.57e+00 angle pdb=" N HIS D 13 " pdb=" CA HIS D 13 " pdb=" C HIS D 13 " ideal model delta sigma weight residual 108.90 110.92 -2.02 1.63e+00 3.76e-01 1.53e+00 angle pdb=" N HIS B 13 " pdb=" CA HIS B 13 " pdb=" C HIS B 13 " ideal model delta sigma weight residual 108.90 110.91 -2.01 1.63e+00 3.76e-01 1.52e+00 angle pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" C HIS E 13 " ideal model delta sigma weight residual 108.90 110.91 -2.01 1.63e+00 3.76e-01 1.52e+00 angle pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" C HIS A 13 " ideal model delta sigma weight residual 108.90 110.90 -2.00 1.63e+00 3.76e-01 1.50e+00 ... (remaining 2030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.81: 725 8.81 - 17.61: 95 17.61 - 26.42: 20 26.42 - 35.22: 0 35.22 - 44.03: 10 Dihedral angle restraints: 850 sinusoidal: 325 harmonic: 525 Sorted by residual: dihedral pdb=" N HIS C 6 " pdb=" CA HIS C 6 " pdb=" CB HIS C 6 " pdb=" CG HIS C 6 " ideal model delta sinusoidal sigma weight residual -180.00 -141.14 -38.86 3 1.50e+01 4.44e-03 6.86e+00 dihedral pdb=" N HIS A 6 " pdb=" CA HIS A 6 " pdb=" CB HIS A 6 " pdb=" CG HIS A 6 " ideal model delta sinusoidal sigma weight residual -180.00 -141.16 -38.84 3 1.50e+01 4.44e-03 6.86e+00 dihedral pdb=" N HIS E 6 " pdb=" CA HIS E 6 " pdb=" CB HIS E 6 " pdb=" CG HIS E 6 " ideal model delta sinusoidal sigma weight residual -180.00 -141.16 -38.84 3 1.50e+01 4.44e-03 6.86e+00 ... (remaining 847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 89 0.025 - 0.050: 81 0.050 - 0.074: 12 0.074 - 0.099: 8 0.099 - 0.124: 20 Chirality restraints: 210 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 207 not shown) Planarity restraints: 270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 18 " 0.001 2.00e-02 2.50e+03 2.89e-03 8.38e-02 pdb=" C VAL A 18 " -0.005 2.00e-02 2.50e+03 pdb=" O VAL A 18 " 0.002 2.00e-02 2.50e+03 pdb=" N PHE A 19 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 18 " 0.001 2.00e-02 2.50e+03 2.88e-03 8.31e-02 pdb=" C VAL C 18 " -0.005 2.00e-02 2.50e+03 pdb=" O VAL C 18 " 0.002 2.00e-02 2.50e+03 pdb=" N PHE C 19 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 18 " 0.001 2.00e-02 2.50e+03 2.86e-03 8.17e-02 pdb=" C VAL B 18 " -0.005 2.00e-02 2.50e+03 pdb=" O VAL B 18 " 0.002 2.00e-02 2.50e+03 pdb=" N PHE B 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 267 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 342 2.79 - 3.32: 1347 3.32 - 3.84: 2220 3.84 - 4.37: 2700 4.37 - 4.90: 5547 Nonbonded interactions: 12156 Sorted by model distance: nonbonded pdb=" O HIS D 14 " pdb=" O GLN E 15 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP D 7 " pdb=" N SER D 8 " model vdw 2.395 2.520 nonbonded pdb=" OD1 ASP E 7 " pdb=" N SER E 8 " model vdw 2.395 2.520 nonbonded pdb=" OD1 ASP A 7 " pdb=" N SER A 8 " model vdw 2.396 2.520 nonbonded pdb=" OD1 ASP C 7 " pdb=" N SER C 8 " model vdw 2.396 2.520 ... (remaining 12151 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' } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 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 : 0.002 0.034 1520 Z= 0.157 Angle : 0.408 2.045 2035 Z= 0.240 Chirality : 0.048 0.124 210 Planarity : 0.001 0.005 270 Dihedral : 9.550 44.027 520 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -4.82 (0.39), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.30), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 13 PHE 0.004 0.001 PHE B 4 TYR 0.003 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.196 Fit side-chains REVERT: A 7 ASP cc_start: 0.6200 (t0) cc_final: 0.5912 (p0) REVERT: A 10 TYR cc_start: 0.7200 (t80) cc_final: 0.6833 (p90) REVERT: A 20 PHE cc_start: 0.7185 (m-80) cc_final: 0.6908 (m-80) REVERT: B 20 PHE cc_start: 0.6862 (m-80) cc_final: 0.6650 (m-80) REVERT: C 10 TYR cc_start: 0.8033 (t80) cc_final: 0.7808 (t80) REVERT: C 23 ASN cc_start: 0.8467 (m-40) cc_final: 0.8188 (p0) REVERT: C 34 LEU cc_start: 0.7478 (tt) cc_final: 0.7191 (tt) REVERT: D 7 ASP cc_start: 0.5072 (t0) cc_final: 0.4091 (m-30) REVERT: D 23 ASN cc_start: 0.8371 (m-40) cc_final: 0.8017 (p0) REVERT: E 13 HIS cc_start: 0.7125 (t-90) cc_final: 0.6919 (p90) REVERT: E 23 ASN cc_start: 0.7074 (m-40) cc_final: 0.5713 (p0) REVERT: E 35 MET cc_start: 0.4910 (ttp) cc_final: 0.4470 (tpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0759 time to fit residues: 7.3478 Evaluate side-chains 56 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 1520 Z= 0.340 Angle : 0.781 4.764 2035 Z= 0.426 Chirality : 0.053 0.166 210 Planarity : 0.004 0.015 270 Dihedral : 5.965 18.754 200 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.22 % Favored : 83.78 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -4.24 (0.47), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.36), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 14 PHE 0.014 0.002 PHE A 4 TYR 0.012 0.004 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 7 ASP cc_start: 0.5839 (t0) cc_final: 0.4856 (m-30) REVERT: C 31 ILE cc_start: 0.9079 (mm) cc_final: 0.8826 (tp) REVERT: D 27 ASN cc_start: 0.8403 (t0) cc_final: 0.7962 (t0) REVERT: E 13 HIS cc_start: 0.6684 (t-90) cc_final: 0.6453 (p-80) REVERT: E 35 MET cc_start: 0.5694 (ttp) cc_final: 0.5131 (tpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0905 time to fit residues: 6.8927 Evaluate side-chains 50 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 1520 Z= 0.315 Angle : 0.730 5.895 2035 Z= 0.395 Chirality : 0.051 0.138 210 Planarity : 0.003 0.014 270 Dihedral : 5.634 18.699 200 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.68 % Favored : 84.32 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -4.32 (0.46), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.35), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS D 13 PHE 0.017 0.002 PHE A 4 TYR 0.013 0.003 TYR D 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.179 Fit side-chains REVERT: A 17 LEU cc_start: 0.8013 (mp) cc_final: 0.7786 (mp) REVERT: B 10 TYR cc_start: 0.7765 (t80) cc_final: 0.7214 (t80) REVERT: D 27 ASN cc_start: 0.8192 (t0) cc_final: 0.7920 (t0) REVERT: E 13 HIS cc_start: 0.6755 (t-90) cc_final: 0.6432 (p-80) REVERT: E 35 MET cc_start: 0.6027 (ttp) cc_final: 0.5250 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0667 time to fit residues: 4.6422 Evaluate side-chains 49 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1520 Z= 0.286 Angle : 0.695 7.576 2035 Z= 0.367 Chirality : 0.048 0.144 210 Planarity : 0.003 0.011 270 Dihedral : 5.505 18.956 200 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -4.29 (0.45), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.34), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 13 PHE 0.014 0.002 PHE D 4 TYR 0.019 0.004 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 TYR cc_start: 0.7785 (t80) cc_final: 0.7103 (t80) REVERT: E 13 HIS cc_start: 0.6728 (t-90) cc_final: 0.6412 (p90) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0641 time to fit residues: 4.5302 Evaluate side-chains 51 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1520 Z= 0.328 Angle : 0.754 8.046 2035 Z= 0.401 Chirality : 0.050 0.144 210 Planarity : 0.003 0.013 270 Dihedral : 5.842 18.993 200 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.92 % Favored : 81.08 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -4.37 (0.44), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.34), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS D 13 PHE 0.016 0.002 PHE A 4 TYR 0.014 0.003 TYR D 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.187 Fit side-chains REVERT: E 10 TYR cc_start: 0.7596 (t80) cc_final: 0.7356 (t80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0662 time to fit residues: 4.5258 Evaluate side-chains 49 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 0.0060 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1520 Z= 0.211 Angle : 0.623 6.056 2035 Z= 0.325 Chirality : 0.047 0.153 210 Planarity : 0.002 0.009 270 Dihedral : 5.360 16.399 200 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.84 % Favored : 82.16 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -4.33 (0.45), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.34), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 14 PHE 0.009 0.001 PHE A 4 TYR 0.012 0.003 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.179 Fit side-chains REVERT: B 7 ASP cc_start: 0.5843 (t0) cc_final: 0.4401 (m-30) REVERT: B 34 LEU cc_start: 0.7323 (tt) cc_final: 0.7060 (tt) REVERT: C 7 ASP cc_start: 0.5697 (t0) cc_final: 0.5352 (t70) REVERT: E 10 TYR cc_start: 0.7571 (t80) cc_final: 0.7306 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0625 time to fit residues: 4.4881 Evaluate side-chains 54 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.6758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1520 Z= 0.238 Angle : 0.682 7.122 2035 Z= 0.352 Chirality : 0.048 0.148 210 Planarity : 0.002 0.009 270 Dihedral : 5.624 15.962 200 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.84 % Favored : 82.16 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -4.34 (0.45), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.35), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 13 PHE 0.011 0.001 PHE B 4 TYR 0.018 0.003 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.175 Fit side-chains REVERT: B 7 ASP cc_start: 0.5882 (t0) cc_final: 0.4465 (m-30) REVERT: B 10 TYR cc_start: 0.7420 (t80) cc_final: 0.6871 (t80) REVERT: C 7 ASP cc_start: 0.5779 (t0) cc_final: 0.5312 (t70) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0602 time to fit residues: 4.2203 Evaluate side-chains 54 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1520 Z= 0.241 Angle : 0.675 8.381 2035 Z= 0.347 Chirality : 0.048 0.150 210 Planarity : 0.002 0.009 270 Dihedral : 5.665 15.772 200 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.47), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.36), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 13 PHE 0.010 0.001 PHE B 4 TYR 0.020 0.003 TYR C 10 ARG 0.003 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 7 ASP cc_start: 0.5947 (t0) cc_final: 0.4400 (m-30) REVERT: B 10 TYR cc_start: 0.7268 (t80) cc_final: 0.6750 (t80) REVERT: C 7 ASP cc_start: 0.5797 (t0) cc_final: 0.5307 (t70) REVERT: E 5 ARG cc_start: 0.7091 (ttt90) cc_final: 0.5234 (pmt-80) REVERT: E 10 TYR cc_start: 0.7532 (t80) cc_final: 0.7088 (t80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0800 time to fit residues: 5.3351 Evaluate side-chains 53 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 0.0870 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1520 Z= 0.228 Angle : 0.648 7.033 2035 Z= 0.331 Chirality : 0.047 0.143 210 Planarity : 0.002 0.010 270 Dihedral : 5.512 15.696 200 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.38 % Favored : 81.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.47), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.36), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 13 PHE 0.009 0.001 PHE B 4 TYR 0.018 0.003 TYR C 10 ARG 0.002 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6032 (t0) cc_final: 0.4436 (m-30) REVERT: B 10 TYR cc_start: 0.7141 (t80) cc_final: 0.6759 (t80) REVERT: C 7 ASP cc_start: 0.5876 (t0) cc_final: 0.5381 (t70) REVERT: D 22 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8214 (mm-40) REVERT: E 5 ARG cc_start: 0.7147 (ttt90) cc_final: 0.5277 (pmt-80) REVERT: E 10 TYR cc_start: 0.7489 (t80) cc_final: 0.6908 (t80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0805 time to fit residues: 5.3810 Evaluate side-chains 54 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1520 Z= 0.211 Angle : 0.678 7.250 2035 Z= 0.334 Chirality : 0.046 0.142 210 Planarity : 0.002 0.010 270 Dihedral : 5.440 15.374 200 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.38 % Favored : 81.62 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -4.18 (0.48), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.37), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.008 0.001 PHE B 4 TYR 0.017 0.003 TYR C 10 ARG 0.001 0.000 ARG E 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 7 ASP cc_start: 0.6001 (t0) cc_final: 0.4602 (m-30) REVERT: B 10 TYR cc_start: 0.7048 (t80) cc_final: 0.6568 (t80) REVERT: E 5 ARG cc_start: 0.7125 (ttt90) cc_final: 0.5311 (pmt-80) REVERT: E 10 TYR cc_start: 0.7506 (t80) cc_final: 0.6780 (t80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0619 time to fit residues: 3.9793 Evaluate side-chains 49 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.158648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.139997 restraints weight = 2835.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.143409 restraints weight = 1384.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.145621 restraints weight = 845.703| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1520 Z= 0.249 Angle : 0.715 7.019 2035 Z= 0.353 Chirality : 0.048 0.140 210 Planarity : 0.003 0.012 270 Dihedral : 5.592 16.261 200 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.92 % Favored : 81.08 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -4.20 (0.48), residues: 185 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.36), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 13 PHE 0.010 0.001 PHE B 4 TYR 0.021 0.003 TYR C 10 ARG 0.002 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 772.36 seconds wall clock time: 15 minutes 35.63 seconds (935.63 seconds total)