Starting phenix.real_space_refine on Wed Mar 5 14:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovm_17223/03_2025/8ovm_17223.cif" } resolution = 3.24 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 865 2.51 5 N 245 2.21 5 O 245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Restraints were copied for chains: C, B, E, D Time building chain proxies: 0.95, per 1000 atoms: 0.70 Number of scatterers: 1360 At special positions: 0 Unit cell: (43.05, 78.75, 43.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 245 8.00 N 245 7.00 C 865 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: 0.77 Conformation dependent library (CDL) restraints added in 161.1 milliseconds 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 23 removed outlier: 6.896A pdb=" N GLU B 11 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 12 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS B 13 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU C 11 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS C 13 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU D 11 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 12 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS D 13 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU E 11 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 12 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS E 13 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.989A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY C 29 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE D 32 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE C 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY D 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE E 32 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE D 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 40 hydrogen bonds defined for protein. 120 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: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 460 1.34 - 1.46: 266 1.46 - 1.57: 649 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1385 Sorted by residual: bond pdb=" N HIS A 6 " pdb=" CA HIS A 6 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.30e+00 bond pdb=" N HIS B 6 " pdb=" CA HIS B 6 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.28e+00 bond pdb=" N HIS E 6 " pdb=" CA HIS E 6 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.15e+00 bond pdb=" N HIS D 6 " pdb=" CA HIS D 6 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.04e+00 bond pdb=" N HIS C 6 " pdb=" CA HIS C 6 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.81e+00 ... (remaining 1380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 1504 0.97 - 1.94: 243 1.94 - 2.92: 48 2.92 - 3.89: 40 3.89 - 4.86: 20 Bond angle restraints: 1855 Sorted by residual: angle pdb=" CA ASP B 7 " pdb=" C ASP B 7 " pdb=" O ASP B 7 " ideal model delta sigma weight residual 121.28 117.17 4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" CA ASP E 7 " pdb=" C ASP E 7 " pdb=" O ASP E 7 " ideal model delta sigma weight residual 121.28 117.18 4.10 1.19e+00 7.06e-01 1.18e+01 angle pdb=" CA ASP A 7 " pdb=" C ASP A 7 " pdb=" O ASP A 7 " ideal model delta sigma weight residual 121.28 117.20 4.08 1.19e+00 7.06e-01 1.18e+01 angle pdb=" CA ASP C 7 " pdb=" C ASP C 7 " pdb=" O ASP C 7 " ideal model delta sigma weight residual 121.28 117.20 4.08 1.19e+00 7.06e-01 1.17e+01 angle pdb=" CA ASP D 7 " pdb=" C ASP D 7 " pdb=" O ASP D 7 " ideal model delta sigma weight residual 121.28 117.21 4.07 1.19e+00 7.06e-01 1.17e+01 ... (remaining 1850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.40: 640 8.40 - 16.80: 75 16.80 - 25.20: 35 25.20 - 33.60: 15 33.60 - 41.99: 10 Dihedral angle restraints: 775 sinusoidal: 295 harmonic: 480 Sorted by residual: dihedral pdb=" CA ILE D 32 " pdb=" CB ILE D 32 " pdb=" CG1 ILE D 32 " pdb=" CD1 ILE D 32 " ideal model delta sinusoidal sigma weight residual 60.00 95.90 -35.90 3 1.50e+01 4.44e-03 6.18e+00 dihedral pdb=" CA ILE A 32 " pdb=" CB ILE A 32 " pdb=" CG1 ILE A 32 " pdb=" CD1 ILE A 32 " ideal model delta sinusoidal sigma weight residual 60.00 95.88 -35.88 3 1.50e+01 4.44e-03 6.18e+00 dihedral pdb=" CA ILE E 32 " pdb=" CB ILE E 32 " pdb=" CG1 ILE E 32 " pdb=" CD1 ILE E 32 " ideal model delta sinusoidal sigma weight residual 60.00 95.87 -35.87 3 1.50e+01 4.44e-03 6.18e+00 ... (remaining 772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 140 0.065 - 0.129: 33 0.129 - 0.194: 17 0.194 - 0.259: 5 0.259 - 0.323: 5 Chirality restraints: 200 Sorted by residual: chirality pdb=" CA VAL C 12 " pdb=" N VAL C 12 " pdb=" C VAL C 12 " pdb=" CB VAL C 12 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL A 12 " pdb=" N VAL A 12 " pdb=" C VAL A 12 " pdb=" CB VAL A 12 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 197 not shown) Planarity restraints: 240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 11 " 0.005 2.00e-02 2.50e+03 9.33e-03 8.70e-01 pdb=" C GLU B 11 " -0.016 2.00e-02 2.50e+03 pdb=" O GLU B 11 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL B 12 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 11 " 0.005 2.00e-02 2.50e+03 9.31e-03 8.67e-01 pdb=" C GLU D 11 " -0.016 2.00e-02 2.50e+03 pdb=" O GLU D 11 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL D 12 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 11 " 0.005 2.00e-02 2.50e+03 9.24e-03 8.54e-01 pdb=" C GLU A 11 " -0.016 2.00e-02 2.50e+03 pdb=" O GLU A 11 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL A 12 " 0.005 2.00e-02 2.50e+03 ... (remaining 237 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 603 2.94 - 3.43: 1190 3.43 - 3.92: 2326 3.92 - 4.41: 2628 4.41 - 4.90: 4740 Nonbonded interactions: 11487 Sorted by model distance: nonbonded pdb=" OE1 GLU A 11 " pdb=" NE2 HIS A 13 " model vdw 2.447 3.120 nonbonded pdb=" OE1 GLU D 11 " pdb=" NE2 HIS D 13 " model vdw 2.447 3.120 nonbonded pdb=" OE1 GLU E 11 " pdb=" NE2 HIS E 13 " model vdw 2.447 3.120 nonbonded pdb=" OE1 GLU C 11 " pdb=" NE2 HIS C 13 " model vdw 2.447 3.120 nonbonded pdb=" OE1 GLU B 11 " pdb=" NE2 HIS B 13 " model vdw 2.447 3.120 ... (remaining 11482 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 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.007 0.037 1385 Z= 0.459 Angle : 0.988 4.858 1855 Z= 0.691 Chirality : 0.090 0.323 200 Planarity : 0.002 0.009 240 Dihedral : 11.001 41.994 475 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.47), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.36), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 13 PHE 0.004 0.001 PHE A 19 TYR 0.004 0.001 TYR B 10 ARG 0.002 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.128 Fit side-chains REVERT: B 22 GLU cc_start: 0.8160 (tt0) cc_final: 0.7825 (tt0) REVERT: B 23 ASP cc_start: 0.8703 (t0) cc_final: 0.8185 (t70) REVERT: D 22 GLU cc_start: 0.8226 (tt0) cc_final: 0.7821 (tt0) REVERT: E 22 GLU cc_start: 0.8011 (tt0) cc_final: 0.7750 (tt0) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1910 time to fit residues: 8.8168 Evaluate side-chains 32 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN D 15 GLN E 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.106787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093007 restraints weight = 2306.274| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.38 r_work: 0.3568 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1385 Z= 0.284 Angle : 0.698 7.463 1855 Z= 0.362 Chirality : 0.052 0.145 200 Planarity : 0.003 0.013 240 Dihedral : 4.996 12.817 185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.57 % Allowed : 15.00 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.49), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.37), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 13 PHE 0.012 0.002 PHE B 20 TYR 0.005 0.001 TYR A 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.154 Fit side-chains REVERT: B 22 GLU cc_start: 0.8833 (tt0) cc_final: 0.8516 (tt0) REVERT: D 22 GLU cc_start: 0.8832 (tt0) cc_final: 0.8487 (tt0) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.1553 time to fit residues: 6.7267 Evaluate side-chains 37 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 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 = 0.3906 r_free = 0.3906 target = 0.108135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.094515 restraints weight = 2237.377| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.37 r_work: 0.3605 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1385 Z= 0.185 Angle : 0.590 6.675 1855 Z= 0.307 Chirality : 0.050 0.138 200 Planarity : 0.002 0.010 240 Dihedral : 4.644 11.348 185 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.29 % Allowed : 16.43 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.49), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 13 PHE 0.007 0.001 PHE B 20 TYR 0.003 0.001 TYR B 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.153 Fit side-chains REVERT: A 26 SER cc_start: 0.8917 (m) cc_final: 0.8650 (p) REVERT: B 22 GLU cc_start: 0.8817 (tt0) cc_final: 0.8445 (tt0) REVERT: D 22 GLU cc_start: 0.8807 (tt0) cc_final: 0.8479 (tt0) outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.1339 time to fit residues: 6.0277 Evaluate side-chains 39 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 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 = 0.3828 r_free = 0.3828 target = 0.104115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.090317 restraints weight = 2322.792| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.36 r_work: 0.3521 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1385 Z= 0.239 Angle : 0.606 7.278 1855 Z= 0.314 Chirality : 0.051 0.136 200 Planarity : 0.002 0.008 240 Dihedral : 4.717 11.855 185 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.71 % Allowed : 17.86 % Favored : 76.43 % 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: -3.37 (0.50), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 6 PHE 0.008 0.002 PHE B 20 TYR 0.005 0.001 TYR B 10 ARG 0.002 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.159 Fit side-chains REVERT: A 26 SER cc_start: 0.8994 (m) cc_final: 0.8739 (p) REVERT: B 22 GLU cc_start: 0.8808 (tt0) cc_final: 0.8404 (tm-30) REVERT: E 23 ASP cc_start: 0.9216 (t0) cc_final: 0.8897 (t0) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1138 time to fit residues: 5.6120 Evaluate side-chains 41 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.0030 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 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 = 0.3833 r_free = 0.3833 target = 0.104548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.090855 restraints weight = 2282.011| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.33 r_work: 0.3533 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1385 Z= 0.237 Angle : 0.613 7.422 1855 Z= 0.312 Chirality : 0.051 0.132 200 Planarity : 0.002 0.008 240 Dihedral : 4.739 11.895 185 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 7.14 % Allowed : 20.71 % Favored : 72.14 % 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: -3.27 (0.51), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 6 PHE 0.008 0.002 PHE B 20 TYR 0.005 0.001 TYR B 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.154 Fit side-chains REVERT: B 22 GLU cc_start: 0.8814 (tt0) cc_final: 0.8412 (tt0) REVERT: B 35 MET cc_start: 0.8211 (ttt) cc_final: 0.7836 (ttp) REVERT: E 23 ASP cc_start: 0.9286 (t0) cc_final: 0.8953 (t0) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.1120 time to fit residues: 5.4089 Evaluate side-chains 42 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 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 = 0.3772 r_free = 0.3772 target = 0.101252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087479 restraints weight = 2302.361| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.30 r_work: 0.3471 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 1385 Z= 0.337 Angle : 0.650 7.098 1855 Z= 0.339 Chirality : 0.052 0.132 200 Planarity : 0.002 0.010 240 Dihedral : 5.060 12.969 185 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 7.14 % Allowed : 22.14 % Favored : 70.71 % 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: -3.26 (0.51), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 6 PHE 0.010 0.002 PHE D 20 TYR 0.007 0.002 TYR B 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.152 Fit side-chains REVERT: C 13 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6156 (m-70) REVERT: E 23 ASP cc_start: 0.9343 (t0) cc_final: 0.8995 (t0) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.0940 time to fit residues: 4.8543 Evaluate side-chains 41 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS ** D 14 HIS ** 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 = 0.3847 r_free = 0.3847 target = 0.105207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.090964 restraints weight = 2319.609| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.35 r_work: 0.3539 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1385 Z= 0.198 Angle : 0.630 7.771 1855 Z= 0.315 Chirality : 0.051 0.131 200 Planarity : 0.002 0.007 240 Dihedral : 4.629 11.376 185 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.43 % Allowed : 23.57 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.53), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 13 PHE 0.007 0.001 PHE B 20 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.158 Fit side-chains REVERT: B 22 GLU cc_start: 0.8828 (tt0) cc_final: 0.8367 (tt0) REVERT: C 13 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.5957 (m-70) REVERT: E 23 ASP cc_start: 0.9250 (t0) cc_final: 0.8968 (t0) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.0990 time to fit residues: 5.2145 Evaluate side-chains 43 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 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 = 0.3842 r_free = 0.3842 target = 0.105122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091065 restraints weight = 2263.209| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.30 r_work: 0.3546 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1385 Z= 0.210 Angle : 0.642 8.259 1855 Z= 0.318 Chirality : 0.051 0.131 200 Planarity : 0.002 0.006 240 Dihedral : 4.582 11.206 185 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 7.86 % Allowed : 21.43 % Favored : 70.71 % 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: -3.22 (0.52), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 6 PHE 0.008 0.002 PHE B 20 TYR 0.004 0.001 TYR B 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.153 Fit side-chains REVERT: A 26 SER cc_start: 0.8978 (m) cc_final: 0.8743 (p) REVERT: B 22 GLU cc_start: 0.8799 (tt0) cc_final: 0.8332 (tt0) REVERT: C 13 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.5982 (m-70) REVERT: E 23 ASP cc_start: 0.9246 (t0) cc_final: 0.8949 (t0) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.1041 time to fit residues: 5.5867 Evaluate side-chains 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS C 14 HIS ** D 14 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.105183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.091364 restraints weight = 2238.693| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.31 r_work: 0.3549 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1385 Z= 0.217 Angle : 0.648 8.297 1855 Z= 0.322 Chirality : 0.051 0.130 200 Planarity : 0.002 0.006 240 Dihedral : 4.564 11.702 185 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.43 % Allowed : 23.57 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.52), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 6 PHE 0.008 0.001 PHE B 20 TYR 0.004 0.001 TYR B 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.146 Fit side-chains REVERT: A 26 SER cc_start: 0.8978 (m) cc_final: 0.8729 (p) REVERT: B 22 GLU cc_start: 0.8805 (tt0) cc_final: 0.8330 (tt0) REVERT: E 23 ASP cc_start: 0.9276 (t0) cc_final: 0.8973 (t0) outliers start: 9 outliers final: 9 residues processed: 43 average time/residue: 0.0981 time to fit residues: 4.9539 Evaluate side-chains 43 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 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 = 0.3885 r_free = 0.3885 target = 0.107682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.093796 restraints weight = 2305.430| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.46 r_work: 0.3597 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1385 Z= 0.160 Angle : 0.628 8.401 1855 Z= 0.308 Chirality : 0.051 0.129 200 Planarity : 0.001 0.004 240 Dihedral : 4.409 13.066 185 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.71 % Allowed : 23.57 % Favored : 70.71 % 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: -3.20 (0.52), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 13 PHE 0.008 0.001 PHE B 20 TYR 0.003 0.001 TYR C 10 ARG 0.001 0.000 ARG B 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 340 Ramachandran restraints generated. 170 Oldfield, 0 Emsley, 170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.126 Fit side-chains REVERT: B 22 GLU cc_start: 0.8767 (tt0) cc_final: 0.8310 (tt0) REVERT: C 13 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.5952 (m-70) REVERT: D 22 GLU cc_start: 0.8852 (tt0) cc_final: 0.8384 (tt0) REVERT: E 23 ASP cc_start: 0.9285 (t0) cc_final: 0.8974 (t0) outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.0962 time to fit residues: 4.6128 Evaluate side-chains 39 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 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 = 0.3865 r_free = 0.3865 target = 0.105564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091270 restraints weight = 2271.166| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.41 r_work: 0.3561 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1385 Z= 0.243 Angle : 0.662 8.360 1855 Z= 0.329 Chirality : 0.051 0.130 200 Planarity : 0.002 0.007 240 Dihedral : 4.571 14.771 185 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 6.43 % Allowed : 25.00 % Favored : 68.57 % 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: -3.23 (0.52), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 14 PHE 0.009 0.002 PHE B 20 TYR 0.005 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.81 seconds wall clock time: 20 minutes 44.86 seconds (1244.86 seconds total)