Starting phenix.real_space_refine on Wed Mar 5 14:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.map" model { file = "/net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otf_17177/03_2025/8otf_17177.cif" } resolution = 3.3 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= 0.001 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 6 5.16 5 C 882 2.51 5 N 234 2.21 5 O 228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1350 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 1.29, per 1000 atoms: 0.96 Number of scatterers: 1350 At special positions: 0 Unit cell: (57.68, 78.28, 29.664, 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 6 16.00 O 228 8.00 N 234 7.00 C 882 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 - 3.00 Amino acid : True - 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: 1.97 Conformation dependent library (CDL) restraints added in 172.2 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 25.8% 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 'C' and resid 24 through 27 removed outlier: 8.682A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.390A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.305A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 20 removed outlier: 6.617A pdb=" N PHE B 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 24 through 27 removed outlier: 8.676A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER F 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN B 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.407A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.265A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.28 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 338 1.33 - 1.45: 255 1.45 - 1.56: 763 1.56 - 1.68: 0 1.68 - 1.79: 12 Bond restraints: 1368 Sorted by residual: bond pdb=" CG HIS F 14 " pdb=" CD2 HIS F 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.43e+00 bond pdb=" CG HIS B 14 " pdb=" CD2 HIS B 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.42e+00 bond pdb=" CG HIS D 14 " pdb=" CD2 HIS D 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.41e+00 bond pdb=" CG HIS A 14 " pdb=" CD2 HIS A 14 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.17e+00 bond pdb=" CG HIS E 14 " pdb=" CD2 HIS E 14 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.14e+00 ... (remaining 1363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 1417 1.57 - 3.15: 338 3.15 - 4.72: 63 4.72 - 6.29: 6 6.29 - 7.87: 12 Bond angle restraints: 1836 Sorted by residual: angle pdb=" CA ASP E 23 " pdb=" CB ASP E 23 " pdb=" CG ASP E 23 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" CA ASP C 23 " pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" CA ASP A 23 " pdb=" CB ASP A 23 " pdb=" CG ASP A 23 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" CA ASP F 23 " pdb=" CB ASP F 23 " pdb=" CG ASP F 23 " ideal model delta sigma weight residual 112.60 120.29 -7.69 1.00e+00 1.00e+00 5.91e+01 angle pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " ideal model delta sigma weight residual 112.60 120.27 -7.67 1.00e+00 1.00e+00 5.89e+01 ... (remaining 1831 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.15: 654 13.15 - 26.29: 75 26.29 - 39.43: 15 39.43 - 52.57: 12 52.57 - 65.71: 12 Dihedral angle restraints: 768 sinusoidal: 276 harmonic: 492 Sorted by residual: dihedral pdb=" CA GLY B 38 " pdb=" C GLY B 38 " pdb=" N VAL B 39 " pdb=" CA VAL B 39 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY D 38 " pdb=" C GLY D 38 " pdb=" N VAL D 39 " pdb=" CA VAL D 39 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY F 38 " pdb=" C GLY F 38 " pdb=" N VAL F 39 " pdb=" CA VAL F 39 " ideal model delta harmonic sigma weight residual 180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 765 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.048: 71 0.048 - 0.092: 67 0.092 - 0.137: 36 0.137 - 0.181: 36 0.181 - 0.226: 12 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA ASP C 23 " pdb=" N ASP C 23 " pdb=" C ASP C 23 " pdb=" CB ASP C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP A 23 " pdb=" N ASP A 23 " pdb=" C ASP A 23 " pdb=" CB ASP A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP E 23 " pdb=" N ASP E 23 " pdb=" C ASP E 23 " pdb=" CB ASP E 23 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 219 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C VAL A 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 40 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 39 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL C 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL C 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 40 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 39 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL E 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL E 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL E 40 " -0.009 2.00e-02 2.50e+03 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 835 3.07 - 3.53: 1302 3.53 - 3.99: 2108 3.99 - 4.44: 2436 4.44 - 4.90: 4177 Nonbonded interactions: 10858 Sorted by model distance: nonbonded pdb=" N GLU E 22 " pdb=" O GLU E 22 " model vdw 2.614 2.496 nonbonded pdb=" N GLU A 22 " pdb=" O GLU A 22 " model vdw 2.614 2.496 nonbonded pdb=" N GLU C 22 " pdb=" O GLU C 22 " model vdw 2.614 2.496 nonbonded pdb=" N VAL F 18 " pdb=" O VAL F 18 " model vdw 2.657 2.496 nonbonded pdb=" N VAL B 18 " pdb=" O VAL B 18 " model vdw 2.658 2.496 ... (remaining 10853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.790 Find NCS groups from input model: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 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 : 0.010 0.047 1368 Z= 0.661 Angle : 1.525 7.866 1836 Z= 1.025 Chirality : 0.102 0.226 222 Planarity : 0.006 0.016 228 Dihedral : 16.154 65.711 456 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.35 % Allowed : 4.35 % Favored : 91.30 % 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: -4.64 (0.33), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 14 PHE 0.014 0.005 PHE F 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.153 Fit side-chains REVERT: A 23 ASP cc_start: 0.8334 (p0) cc_final: 0.8108 (p0) REVERT: A 35 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8845 (tpt) REVERT: D 16 LYS cc_start: 0.8968 (mttp) cc_final: 0.8203 (mmtt) REVERT: E 22 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6818 (pt0) REVERT: E 23 ASP cc_start: 0.8576 (p0) cc_final: 0.8324 (p0) REVERT: F 22 GLU cc_start: 0.8889 (mm-30) cc_final: 0.7005 (pt0) outliers start: 6 outliers final: 0 residues processed: 36 average time/residue: 0.1756 time to fit residues: 6.9757 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.100693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081497 restraints weight = 2026.507| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.81 r_work: 0.3186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1368 Z= 0.104 Angle : 0.420 2.477 1836 Z= 0.238 Chirality : 0.055 0.130 222 Planarity : 0.001 0.006 228 Dihedral : 8.487 59.674 186 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.62 % Allowed : 7.25 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.42), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 14 PHE 0.005 0.001 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.141 Fit side-chains REVERT: D 22 GLU cc_start: 0.8412 (tp30) cc_final: 0.8176 (tp30) REVERT: E 22 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6223 (pt0) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.1522 time to fit residues: 6.0746 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.105586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084991 restraints weight = 1939.703| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.98 r_work: 0.3221 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1368 Z= 0.123 Angle : 0.376 2.063 1836 Z= 0.209 Chirality : 0.054 0.127 222 Planarity : 0.001 0.004 228 Dihedral : 7.507 72.994 183 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 7.97 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.48), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.37), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 14 PHE 0.005 0.001 PHE D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.154 Fit side-chains REVERT: D 22 GLU cc_start: 0.8335 (tp30) cc_final: 0.7869 (mm-30) REVERT: E 12 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8011 (p) REVERT: E 22 GLU cc_start: 0.8219 (mm-30) cc_final: 0.6232 (pt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1540 time to fit residues: 5.8518 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 16 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.099472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080691 restraints weight = 2097.033| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.91 r_work: 0.3165 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 1368 Z= 0.240 Angle : 0.421 2.607 1836 Z= 0.228 Chirality : 0.054 0.131 222 Planarity : 0.001 0.004 228 Dihedral : 4.190 10.284 180 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 9.42 % Favored : 87.68 % 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: -1.78 (0.52), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.007 0.001 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.157 Fit side-chains REVERT: D 22 GLU cc_start: 0.8533 (tp30) cc_final: 0.8150 (mm-30) REVERT: E 22 GLU cc_start: 0.8273 (mm-30) cc_final: 0.6282 (pt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1582 time to fit residues: 6.1447 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.0050 chunk 17 optimal weight: 0.0270 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088643 restraints weight = 1913.021| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.95 r_work: 0.3305 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1368 Z= 0.151 Angle : 0.374 2.616 1836 Z= 0.205 Chirality : 0.054 0.128 222 Planarity : 0.001 0.007 228 Dihedral : 3.927 9.901 180 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 9.42 % Favored : 87.68 % 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: -1.51 (0.55), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 14 PHE 0.005 0.001 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.157 Fit side-chains REVERT: D 22 GLU cc_start: 0.8392 (tp30) cc_final: 0.7978 (mm-30) REVERT: E 22 GLU cc_start: 0.8276 (mm-30) cc_final: 0.6302 (pt0) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.1748 time to fit residues: 7.3002 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079810 restraints weight = 2097.934| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.94 r_work: 0.3143 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1368 Z= 0.301 Angle : 0.456 2.894 1836 Z= 0.248 Chirality : 0.054 0.131 222 Planarity : 0.001 0.008 228 Dihedral : 4.161 11.179 180 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 11.59 % Favored : 85.51 % 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 (0.56), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 13 PHE 0.007 0.002 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.154 Fit side-chains REVERT: D 22 GLU cc_start: 0.8567 (tp30) cc_final: 0.8177 (mm-30) REVERT: E 22 GLU cc_start: 0.8246 (mm-30) cc_final: 0.6245 (pt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1620 time to fit residues: 6.3025 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082203 restraints weight = 2082.703| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.98 r_work: 0.3175 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1368 Z= 0.156 Angle : 0.387 3.006 1836 Z= 0.213 Chirality : 0.053 0.128 222 Planarity : 0.001 0.007 228 Dihedral : 3.842 10.177 180 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 12.32 % Favored : 85.51 % 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: -1.29 (0.56), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 13 PHE 0.005 0.001 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.174 Fit side-chains REVERT: D 22 GLU cc_start: 0.8398 (tp30) cc_final: 0.7979 (mm-30) REVERT: E 22 GLU cc_start: 0.8236 (mm-30) cc_final: 0.6243 (pt0) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1770 time to fit residues: 6.7049 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 3 optimal weight: 0.6980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.102313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082772 restraints weight = 2089.679| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.95 r_work: 0.3203 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1368 Z= 0.159 Angle : 0.386 3.064 1836 Z= 0.212 Chirality : 0.053 0.128 222 Planarity : 0.001 0.007 228 Dihedral : 3.713 10.255 180 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 12.32 % Favored : 84.78 % 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: -1.16 (0.56), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 13 PHE 0.004 0.001 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.129 Fit side-chains REVERT: D 22 GLU cc_start: 0.8379 (tp30) cc_final: 0.7984 (mm-30) REVERT: E 22 GLU cc_start: 0.8292 (mm-30) cc_final: 0.6290 (pt0) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.1639 time to fit residues: 6.3451 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079501 restraints weight = 2059.685| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.95 r_work: 0.3149 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1368 Z= 0.296 Angle : 0.453 3.195 1836 Z= 0.246 Chirality : 0.054 0.131 222 Planarity : 0.001 0.006 228 Dihedral : 3.961 10.450 180 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 13.04 % Favored : 84.06 % 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: -1.01 (0.57), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 13 PHE 0.008 0.002 PHE B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.138 Fit side-chains REVERT: D 22 GLU cc_start: 0.8539 (tp30) cc_final: 0.8151 (mm-30) REVERT: E 22 GLU cc_start: 0.8323 (mm-30) cc_final: 0.6327 (pt0) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.1522 time to fit residues: 5.9219 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079201 restraints weight = 2096.020| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.94 r_work: 0.3139 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1368 Z= 0.309 Angle : 0.457 3.292 1836 Z= 0.248 Chirality : 0.054 0.131 222 Planarity : 0.001 0.006 228 Dihedral : 4.005 10.460 180 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % 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: -0.88 (0.57), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 13 PHE 0.008 0.002 PHE B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.159 Fit side-chains REVERT: D 22 GLU cc_start: 0.8547 (tp30) cc_final: 0.8143 (mm-30) REVERT: E 22 GLU cc_start: 0.8338 (mm-30) cc_final: 0.6359 (pt0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1591 time to fit residues: 6.3672 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078862 restraints weight = 2093.365| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.03 r_work: 0.3121 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 1368 Z= 0.312 Angle : 0.469 3.295 1836 Z= 0.254 Chirality : 0.054 0.131 222 Planarity : 0.001 0.006 228 Dihedral : 4.049 10.550 180 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.45 % Allowed : 15.22 % Favored : 83.33 % 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: -0.79 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 13 PHE 0.008 0.002 PHE B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1264.08 seconds wall clock time: 22 minutes 32.52 seconds (1352.52 seconds total)