Starting phenix.real_space_refine on Mon Feb 10 19:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otf_17177/02_2025/8otf_17177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otf_17177/02_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_17177/02_2025/8otf_17177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otf_17177/02_2025/8otf_17177.map" model { file = "/net/cci-nas-00/data/ceres_data/8otf_17177/02_2025/8otf_17177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otf_17177/02_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-5592/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: 1.13, per 1000 atoms: 0.84 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: 1.19 Conformation dependent library (CDL) restraints added in 229.6 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: 1.19 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: 2.700 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: 9.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- 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 : 0.209 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: 0.1736 time to fit residues: 6.9024 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** 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 = 0.3610 r_free = 0.3610 target = 0.101631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081918 restraints weight = 1989.236| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.86 r_work: 0.3184 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1368 Z= 0.102 Angle : 0.420 2.518 1836 Z= 0.238 Chirality : 0.055 0.130 222 Planarity : 0.001 0.006 228 Dihedral : 8.512 59.805 186 Min Nonbonded Distance : 2.639 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: -2.95 (0.43), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.33), 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 40 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.157 Fit side-chains REVERT: D 22 GLU cc_start: 0.8408 (tp30) cc_final: 0.8157 (tp30) REVERT: E 22 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6223 (pt0) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.1621 time to fit residues: 6.3076 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 : 0.154 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.107794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087288 restraints weight = 1934.994| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.94 r_work: 0.3262 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2959 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= 0.115 Angle : 0.370 2.355 1836 Z= 0.204 Chirality : 0.053 0.125 222 Planarity : 0.001 0.005 228 Dihedral : 7.468 74.870 183 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.90 % Allowed : 6.52 % Favored : 90.58 % 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: -2.26 (0.49), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 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 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.156 Fit side-chains REVERT: C 22 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: D 22 GLU cc_start: 0.8289 (tp30) cc_final: 0.7826 (mm-30) REVERT: E 12 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8072 (p) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 0.1511 time to fit residues: 5.6044 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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: 0.0470 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.100387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081361 restraints weight = 2086.202| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.93 r_work: 0.3176 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1368 Z= 0.215 Angle : 0.402 2.446 1836 Z= 0.219 Chirality : 0.053 0.132 222 Planarity : 0.001 0.008 228 Dihedral : 4.052 10.237 180 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.62 % Allowed : 7.97 % Favored : 88.41 % 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: -1.76 (0.52), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 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: 5 poor density : 34 time to evaluate : 0.157 Fit side-chains REVERT: D 22 GLU cc_start: 0.8478 (tp30) cc_final: 0.8005 (mm-30) REVERT: E 22 GLU cc_start: 0.8360 (mm-30) cc_final: 0.6376 (pt0) outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.1468 time to fit residues: 5.6014 Evaluate side-chains 36 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 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: 0.8980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.109161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089746 restraints weight = 1901.383| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.92 r_work: 0.3316 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3126 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= 0.133 Angle : 0.365 2.640 1836 Z= 0.202 Chirality : 0.054 0.127 222 Planarity : 0.001 0.006 228 Dihedral : 3.833 9.934 180 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.62 % Allowed : 8.70 % 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: -1.55 (0.55), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 13 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 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: 0.8344 (tp30) cc_final: 0.7872 (mm-30) REVERT: E 22 GLU cc_start: 0.8354 (mm-30) cc_final: 0.6369 (pt0) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.1707 time to fit residues: 6.7830 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 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: 1.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080667 restraints weight = 2070.108| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.95 r_work: 0.3174 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3034 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= 0.253 Angle : 0.419 2.912 1836 Z= 0.229 Chirality : 0.054 0.131 222 Planarity : 0.001 0.008 228 Dihedral : 4.015 11.120 180 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.99 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: -1.37 (0.55), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.42), 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 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.158 Fit side-chains REVERT: D 22 GLU cc_start: 0.8535 (tp30) cc_final: 0.8082 (mm-30) REVERT: E 22 GLU cc_start: 0.8392 (mm-30) cc_final: 0.6356 (pt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1593 time to fit residues: 6.0816 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 : 0.155 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** 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 = 0.3650 r_free = 0.3650 target = 0.102873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082926 restraints weight = 2046.164| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.95 r_work: 0.3191 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3204 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= 0.148 Angle : 0.374 2.992 1836 Z= 0.207 Chirality : 0.053 0.127 222 Planarity : 0.001 0.007 228 Dihedral : 3.777 10.047 180 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 10.14 % Favored : 86.96 % 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: -1.25 (0.56), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (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 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 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.141 Fit side-chains REVERT: C 22 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: D 22 GLU cc_start: 0.8387 (tp30) cc_final: 0.7994 (mm-30) REVERT: E 22 GLU cc_start: 0.8364 (mm-30) cc_final: 0.6363 (pt0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1507 time to fit residues: 5.7677 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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=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: 8.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3596 r_free = 0.3596 target = 0.099166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079472 restraints weight = 2124.156| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.97 r_work: 0.3150 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3068 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= 0.278 Angle : 0.436 3.063 1836 Z= 0.237 Chirality : 0.054 0.130 222 Planarity : 0.001 0.007 228 Dihedral : 3.976 11.047 180 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.62 % Allowed : 11.59 % 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: -1.14 (0.56), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 13 PHE 0.007 0.002 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 40 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.117 Fit side-chains REVERT: D 22 GLU cc_start: 0.8539 (tp30) cc_final: 0.8144 (mm-30) REVERT: E 22 GLU cc_start: 0.8406 (mm-30) cc_final: 0.6346 (pt0) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.1631 time to fit residues: 6.3446 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 : 0.160 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS D 14 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078373 restraints weight = 2076.070| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.91 r_work: 0.3119 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 1368 Z= 0.349 Angle : 0.475 3.122 1836 Z= 0.257 Chirality : 0.054 0.132 222 Planarity : 0.002 0.007 228 Dihedral : 4.143 11.402 180 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.90 % Allowed : 14.49 % 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: -0.98 (0.57), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 13 PHE 0.009 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 40 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.129 Fit side-chains REVERT: D 22 GLU cc_start: 0.8581 (tp30) cc_final: 0.8139 (mm-30) REVERT: E 22 GLU cc_start: 0.8400 (mm-30) cc_final: 0.6383 (pt0) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1352 time to fit residues: 5.4136 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 : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU 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: 5.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3595 r_free = 0.3595 target = 0.100933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081246 restraints weight = 2056.218| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.95 r_work: 0.3155 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1368 Z= 0.193 Angle : 0.417 3.244 1836 Z= 0.228 Chirality : 0.053 0.128 222 Planarity : 0.001 0.006 228 Dihedral : 3.914 11.145 180 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 15.94 % Favored : 81.88 % 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: -0.90 (0.57), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 13 PHE 0.005 0.001 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 : 0.218 Fit side-chains REVERT: D 22 GLU cc_start: 0.8461 (tp30) cc_final: 0.7989 (mm-30) REVERT: E 22 GLU cc_start: 0.8391 (mm-30) cc_final: 0.6375 (pt0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1724 time to fit residues: 6.8477 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3640 r_free = 0.3640 target = 0.103411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083305 restraints weight = 2010.325| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.92 r_work: 0.3214 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1368 Z= 0.138 Angle : 0.398 3.288 1836 Z= 0.218 Chirality : 0.053 0.126 222 Planarity : 0.001 0.006 228 Dihedral : 3.700 10.928 180 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.72 % Allowed : 15.22 % 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: -0.78 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.58 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 13 PHE 0.004 0.001 PHE D 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.58 seconds wall clock time: 21 minutes 59.03 seconds (1319.03 seconds total)