Starting phenix.real_space_refine on Thu Dec 7 16:23:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olq_16961/12_2023/8olq_16961.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 800 2.51 5 N 235 2.21 5 O 225 1.98 5 H 1185 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2445 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 489 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 489 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 489 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 489 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 489 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Time building chain proxies: 1.53, per 1000 atoms: 0.63 Number of scatterers: 2445 At special positions: 0 Unit cell: (55.752, 43.632, 46.864, 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) O 225 8.00 N 235 7.00 C 800 6.00 H 1185 1.00 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: 1.75 Conformation dependent library (CDL) restraints added in 393.1 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 6.755A pdb=" N GLU A 3 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N HIS B 6 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG A 5 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU C 3 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N HIS D 6 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 5 " --> pdb=" O HIS D 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.701A pdb=" N VAL A 12 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.925A pdb=" N LEU A 17 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 17 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 17 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 17 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 27 removed outlier: 5.899A pdb=" N GLY A 25 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY B 25 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY C 25 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY D 25 " --> pdb=" O SER E 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.446A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 16 hydrogen bonds defined for protein. 48 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: 0.72 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 1185 0.98 - 1.12: 0 1.12 - 1.26: 210 1.26 - 1.40: 390 1.40 - 1.54: 690 Bond restraints: 2475 Sorted by residual: bond pdb=" N ALA B 2 " pdb=" CA ALA B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ALA C 2 " pdb=" CA ALA C 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ALA E 2 " pdb=" CA ALA E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ALA D 2 " pdb=" CA ALA D 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ALA A 2 " pdb=" CA ALA A 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 2470 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.11: 2475 111.11 - 116.15: 509 116.15 - 121.18: 787 121.18 - 126.22: 589 126.22 - 131.25: 45 Bond angle restraints: 4405 Sorted by residual: angle pdb=" CA ALA E 2 " pdb=" N ALA E 2 " pdb=" H ALA E 2 " ideal model delta sigma weight residual 114.00 109.47 4.53 3.00e+00 1.11e-01 2.28e+00 angle pdb=" CA ALA A 2 " pdb=" N ALA A 2 " pdb=" H ALA A 2 " ideal model delta sigma weight residual 114.00 109.49 4.51 3.00e+00 1.11e-01 2.26e+00 angle pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N GLY A 9 " ideal model delta sigma weight residual 115.51 117.46 -1.95 1.30e+00 5.92e-01 2.26e+00 angle pdb=" CA ALA B 2 " pdb=" N ALA B 2 " pdb=" H ALA B 2 " ideal model delta sigma weight residual 114.00 109.50 4.50 3.00e+00 1.11e-01 2.25e+00 angle pdb=" CA ALA C 2 " pdb=" N ALA C 2 " pdb=" H ALA C 2 " ideal model delta sigma weight residual 114.00 109.50 4.50 3.00e+00 1.11e-01 2.25e+00 ... (remaining 4400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.41: 950 7.41 - 14.81: 110 14.81 - 22.22: 40 22.22 - 29.62: 10 29.62 - 37.03: 5 Dihedral angle restraints: 1115 sinusoidal: 535 harmonic: 580 Sorted by residual: dihedral pdb=" CA ASP A 7 " pdb=" C ASP A 7 " pdb=" N SER A 8 " pdb=" CA SER A 8 " ideal model delta harmonic sigma weight residual 180.00 169.64 10.36 0 5.00e+00 4.00e-02 4.29e+00 dihedral pdb=" CA ASP C 7 " pdb=" C ASP C 7 " pdb=" N SER C 8 " pdb=" CA SER C 8 " ideal model delta harmonic sigma weight residual 180.00 169.66 10.34 0 5.00e+00 4.00e-02 4.28e+00 dihedral pdb=" CA ASP B 7 " pdb=" C ASP B 7 " pdb=" N SER B 8 " pdb=" CA SER B 8 " ideal model delta harmonic sigma weight residual 180.00 169.69 10.31 0 5.00e+00 4.00e-02 4.26e+00 ... (remaining 1112 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.025: 99 0.025 - 0.050: 36 0.050 - 0.075: 15 0.075 - 0.100: 5 0.100 - 0.124: 15 Chirality restraints: 170 Sorted by residual: chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 12 " pdb=" N VAL A 12 " pdb=" C VAL A 12 " pdb=" CB VAL A 12 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 32 " pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CB ILE A 32 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 167 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 23 " 0.002 2.00e-02 2.50e+03 2.08e-03 6.47e-02 pdb=" CG ASN D 23 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN D 23 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 23 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 23 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN D 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 23 " 0.002 2.00e-02 2.50e+03 2.00e-03 6.02e-02 pdb=" CG ASN C 23 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN C 23 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 23 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 23 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN C 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 23 " -0.001 2.00e-02 2.50e+03 1.84e-03 5.09e-02 pdb=" CG ASN B 23 " 0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN B 23 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 23 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 23 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN B 23 " -0.001 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.24: 250 2.24 - 2.81: 5059 2.81 - 3.37: 5625 3.37 - 3.94: 8026 3.94 - 4.50: 11867 Nonbonded interactions: 30827 Sorted by model distance: nonbonded pdb=" OE2 GLU D 11 " pdb=" HG SER E 26 " model vdw 1.677 1.850 nonbonded pdb=" OE2 GLU B 11 " pdb=" HG SER C 26 " model vdw 1.721 1.850 nonbonded pdb=" O GLN A 22 " pdb=" H ASN B 23 " model vdw 1.749 1.850 nonbonded pdb="HD21 ASN B 23 " pdb=" OD1 ASN B 27 " model vdw 1.756 1.850 nonbonded pdb="HD21 ASN A 23 " pdb=" OD1 ASN A 27 " model vdw 1.756 1.850 ... (remaining 30822 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: 0.710 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: 0.040 Extract box with map and model: 3.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.900 Find NCS groups from input model: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.003 0.033 1290 Z= 0.192 Angle : 0.489 2.040 1725 Z= 0.321 Chirality : 0.048 0.124 170 Planarity : 0.001 0.003 230 Dihedral : 7.644 23.346 440 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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: -0.52 (0.70), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 6 PHE 0.003 0.001 PHE D 19 TYR 0.002 0.001 TYR B 10 ARG 0.000 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2287 time to fit residues: 12.1093 Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2368 ------------------------------------------------------------------------------- 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: 5.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1290 Z= 0.171 Angle : 0.482 4.428 1725 Z= 0.277 Chirality : 0.051 0.130 170 Planarity : 0.002 0.020 230 Dihedral : 4.543 14.531 165 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.80 % Allowed : 12.80 % Favored : 86.40 % 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: -0.91 (0.67), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 6 PHE 0.012 0.002 PHE E 20 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1373 time to fit residues: 6.4393 Evaluate side-chains 35 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.226 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0478 time to fit residues: 0.3231 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1290 Z= 0.173 Angle : 0.451 2.183 1725 Z= 0.273 Chirality : 0.049 0.125 170 Planarity : 0.002 0.010 230 Dihedral : 4.741 14.192 165 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.20 % Allowed : 15.20 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.64), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 6 PHE 0.011 0.002 PHE E 20 TYR 0.005 0.002 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1266 time to fit residues: 5.6767 Evaluate side-chains 36 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.224 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0463 time to fit residues: 0.4541 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1290 Z= 0.122 Angle : 0.407 2.038 1725 Z= 0.245 Chirality : 0.049 0.126 170 Planarity : 0.001 0.007 230 Dihedral : 4.394 12.876 165 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.60 % Allowed : 16.00 % Favored : 82.40 % 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: -1.42 (0.63), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 6 PHE 0.009 0.001 PHE E 20 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1349 time to fit residues: 5.6772 Evaluate side-chains 34 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.222 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0474 time to fit residues: 0.3265 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1290 Z= 0.111 Angle : 0.388 1.915 1725 Z= 0.235 Chirality : 0.049 0.125 170 Planarity : 0.001 0.006 230 Dihedral : 4.197 13.623 165 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.00 % Allowed : 16.00 % Favored : 80.00 % 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: -1.37 (0.64), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 6 PHE 0.010 0.001 PHE E 20 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.1494 time to fit residues: 6.9201 Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.230 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.0503 time to fit residues: 0.4193 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1290 Z= 0.114 Angle : 0.387 1.847 1725 Z= 0.236 Chirality : 0.049 0.125 170 Planarity : 0.001 0.005 230 Dihedral : 4.066 12.755 165 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % 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: -1.33 (0.65), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 6 PHE 0.011 0.002 PHE A 19 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1366 time to fit residues: 6.0693 Evaluate side-chains 38 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.193 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0506 time to fit residues: 0.4053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1290 Z= 0.107 Angle : 0.382 2.636 1725 Z= 0.231 Chirality : 0.049 0.125 170 Planarity : 0.001 0.005 230 Dihedral : 3.894 13.230 165 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % 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: -1.42 (0.65), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 6 PHE 0.009 0.002 PHE A 19 TYR 0.004 0.001 TYR E 10 ARG 0.000 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.1260 time to fit residues: 5.5079 Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.214 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0460 time to fit residues: 0.4049 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 0 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1290 Z= 0.132 Angle : 0.390 2.019 1725 Z= 0.238 Chirality : 0.049 0.124 170 Planarity : 0.001 0.005 230 Dihedral : 3.966 12.841 165 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.40 % Allowed : 18.40 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.65), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 6 PHE 0.010 0.002 PHE B 20 TYR 0.004 0.001 TYR B 10 ARG 0.000 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1365 time to fit residues: 6.1121 Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.220 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.0479 time to fit residues: 0.3823 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1290 Z= 0.125 Angle : 0.387 1.856 1725 Z= 0.236 Chirality : 0.049 0.124 170 Planarity : 0.001 0.007 230 Dihedral : 3.919 13.593 165 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.40 % Allowed : 19.20 % Favored : 78.40 % 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: -1.46 (0.66), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 6 PHE 0.015 0.002 PHE E 19 TYR 0.004 0.001 TYR B 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.1322 time to fit residues: 5.5703 Evaluate side-chains 36 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.195 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.0442 time to fit residues: 0.3574 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1290 Z= 0.107 Angle : 0.379 1.890 1725 Z= 0.233 Chirality : 0.049 0.125 170 Planarity : 0.001 0.005 230 Dihedral : 3.616 12.172 165 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.40 % Allowed : 20.00 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.66), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 6 PHE 0.012 0.001 PHE B 20 TYR 0.003 0.001 TYR B 10 ARG 0.001 0.000 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.1369 time to fit residues: 5.7593 Evaluate side-chains 36 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.212 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.0460 time to fit residues: 0.3834 ------------------------------------------------------------------------------- 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: 10.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.151267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131029 restraints weight = 6105.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.135932 restraints weight = 3025.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.139524 restraints weight = 1796.374| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1290 Z= 0.128 Angle : 0.384 1.767 1725 Z= 0.235 Chirality : 0.049 0.124 170 Planarity : 0.001 0.005 230 Dihedral : 3.739 13.004 165 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.40 % Allowed : 20.00 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.67), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 6 PHE 0.009 0.001 PHE B 20 TYR 0.004 0.001 TYR B 10 ARG 0.000 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.70 seconds wall clock time: 36 minutes 11.57 seconds (2171.57 seconds total)