Starting phenix.real_space_refine on Fri Oct 10 10:15:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovm_17223/10_2025/8ovm_17223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovm_17223/10_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_17223/10_2025/8ovm_17223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovm_17223/10_2025/8ovm_17223.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovm_17223/10_2025/8ovm_17223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovm_17223/10_2025/8ovm_17223.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: B, C, D, E Time building chain proxies: 0.27, per 1000 atoms: 0.20 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: 0.05 Conformation dependent library (CDL) restraints added in 31.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.03 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: 0.09 Time building geometry restraints manager: 0.07 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.730 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 1.900 Find NCS groups from input model: 0.010 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:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.370 ------------------------------------------------------------------------------- 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= 0.456 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.001 ARG E 5 TYR 0.004 0.001 TYR B 10 PHE 0.004 0.001 PHE A 19 HIS 0.001 0.000 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 1385) covalent geometry : angle 0.98827 ( 1855) hydrogen bonds : bond 0.18808 ( 40) hydrogen bonds : angle 9.59388 ( 120) *********************** 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 : 0.029 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: 0.0503 time to fit residues: 2.3155 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 : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.104567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.091256 restraints weight = 2329.585| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.30 r_work: 0.3539 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3861 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= 0.221 Angle : 0.725 7.721 1855 Z= 0.379 Chirality : 0.053 0.147 200 Planarity : 0.003 0.015 240 Dihedral : 5.225 13.740 185 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.57 % Allowed : 15.71 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.49), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.37), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.006 0.001 TYR A 10 PHE 0.014 0.002 PHE B 20 HIS 0.003 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 1385) covalent geometry : angle 0.72487 ( 1855) hydrogen bonds : bond 0.04738 ( 40) hydrogen bonds : angle 6.61984 ( 120) *********************** 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 41 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.028 Fit side-chains REVERT: B 22 GLU cc_start: 0.8845 (tt0) cc_final: 0.8496 (tt0) REVERT: D 22 GLU cc_start: 0.8797 (tt0) cc_final: 0.8457 (tt0) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.0422 time to fit residues: 1.8610 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 : 0.028 ------------------------------------------------------------------------------- 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 9 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.103057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089329 restraints weight = 2329.675| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.33 r_work: 0.3510 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1385 Z= 0.192 Angle : 0.633 6.486 1855 Z= 0.336 Chirality : 0.051 0.138 200 Planarity : 0.002 0.009 240 Dihedral : 5.047 12.954 185 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.00 % Allowed : 17.86 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.49), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.37), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.006 0.001 TYR D 10 PHE 0.008 0.002 PHE B 20 HIS 0.001 0.000 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 1385) covalent geometry : angle 0.63308 ( 1855) hydrogen bonds : bond 0.03809 ( 40) hydrogen bonds : angle 6.07037 ( 120) *********************** 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 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.031 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.0300 time to fit residues: 1.5267 Evaluate side-chains 40 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.030 ------------------------------------------------------------------------------- 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 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.103270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.089503 restraints weight = 2347.016| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.33 r_work: 0.3505 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1385 Z= 0.177 Angle : 0.607 6.969 1855 Z= 0.320 Chirality : 0.051 0.134 200 Planarity : 0.002 0.006 240 Dihedral : 4.875 12.660 185 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.71 % Allowed : 22.86 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.50), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.005 0.001 TYR B 10 PHE 0.008 0.002 PHE D 20 HIS 0.002 0.000 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 1385) covalent geometry : angle 0.60710 ( 1855) hydrogen bonds : bond 0.03218 ( 40) hydrogen bonds : angle 5.97354 ( 120) *********************** 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 43 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.059 Fit side-chains REVERT: B 22 GLU cc_start: 0.8754 (tt0) cc_final: 0.8236 (tt0) REVERT: C 5 ARG cc_start: 0.4303 (mpt180) cc_final: 0.4052 (mpp-170) REVERT: E 23 ASP cc_start: 0.9226 (t0) cc_final: 0.8988 (t0) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.0567 time to fit residues: 2.6966 Evaluate side-chains 42 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.053 ------------------------------------------------------------------------------- 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 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.0030 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.103250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.089682 restraints weight = 2362.591| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.33 r_work: 0.3512 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1385 Z= 0.181 Angle : 0.601 7.532 1855 Z= 0.318 Chirality : 0.051 0.132 200 Planarity : 0.002 0.007 240 Dihedral : 4.820 12.608 185 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.43 % Allowed : 22.14 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.51), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.006 0.001 TYR B 10 PHE 0.009 0.002 PHE B 20 HIS 0.002 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 1385) covalent geometry : angle 0.60054 ( 1855) hydrogen bonds : bond 0.03148 ( 40) hydrogen bonds : angle 5.90498 ( 120) *********************** 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 45 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.057 Fit side-chains REVERT: B 22 GLU cc_start: 0.8774 (tt0) cc_final: 0.8268 (tt0) REVERT: C 13 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6108 (m-70) REVERT: E 23 ASP cc_start: 0.9278 (t0) cc_final: 0.8998 (t0) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.0499 time to fit residues: 2.5163 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 : 0.051 ------------------------------------------------------------------------------- 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 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.104010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.090980 restraints weight = 2313.078| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.27 r_work: 0.3546 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1385 Z= 0.148 Angle : 0.630 7.668 1855 Z= 0.316 Chirality : 0.051 0.131 200 Planarity : 0.002 0.005 240 Dihedral : 4.625 12.116 185 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.14 % Allowed : 21.43 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.51), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.004 0.001 TYR B 10 PHE 0.008 0.002 PHE B 20 HIS 0.002 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 1385) covalent geometry : angle 0.63000 ( 1855) hydrogen bonds : bond 0.02893 ( 40) hydrogen bonds : angle 5.76624 ( 120) *********************** 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 46 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.055 Fit side-chains REVERT: B 22 GLU cc_start: 0.8782 (tt0) cc_final: 0.8304 (tt0) REVERT: B 35 MET cc_start: 0.8877 (ttp) cc_final: 0.8660 (ttp) REVERT: C 13 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.5985 (m-70) REVERT: E 23 ASP cc_start: 0.9306 (t0) cc_final: 0.9021 (t0) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.0518 time to fit residues: 2.6777 Evaluate side-chains 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.086801 restraints weight = 2320.300| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.28 r_work: 0.3460 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 1385 Z= 0.265 Angle : 0.689 7.319 1855 Z= 0.358 Chirality : 0.052 0.130 200 Planarity : 0.002 0.006 240 Dihedral : 5.029 13.248 185 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 8.57 % Allowed : 22.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.51), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.008 0.002 TYR B 10 PHE 0.010 0.002 PHE D 20 HIS 0.003 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 1385) covalent geometry : angle 0.68856 ( 1855) hydrogen bonds : bond 0.03568 ( 40) hydrogen bonds : angle 6.11621 ( 120) *********************** 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 48 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.057 Fit side-chains REVERT: C 13 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6246 (m-70) REVERT: E 23 ASP cc_start: 0.9299 (t0) cc_final: 0.9011 (t0) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.0425 time to fit residues: 2.3481 Evaluate side-chains 43 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.061 ------------------------------------------------------------------------------- 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 C residue 34 LEU 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 7 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.103408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089348 restraints weight = 2258.435| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.34 r_work: 0.3515 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5527 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= 0.149 Angle : 0.691 8.397 1855 Z= 0.335 Chirality : 0.051 0.129 200 Planarity : 0.002 0.007 240 Dihedral : 4.619 11.882 185 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.52), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.005 0.001 TYR B 10 PHE 0.008 0.002 PHE B 20 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 1385) covalent geometry : angle 0.69121 ( 1855) hydrogen bonds : bond 0.03012 ( 40) hydrogen bonds : angle 5.78933 ( 120) *********************** 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 45 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.058 Fit side-chains REVERT: A 5 ARG cc_start: 0.3910 (pmt-80) cc_final: 0.3699 (pmt-80) REVERT: B 22 GLU cc_start: 0.8761 (tt0) cc_final: 0.8316 (tt0) REVERT: C 13 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6093 (m-70) REVERT: E 23 ASP cc_start: 0.9230 (t0) cc_final: 0.8933 (t0) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.0449 time to fit residues: 2.3096 Evaluate side-chains 42 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 13 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.106344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092250 restraints weight = 2274.334| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.35 r_work: 0.3572 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1385 Z= 0.110 Angle : 0.657 8.292 1855 Z= 0.314 Chirality : 0.051 0.129 200 Planarity : 0.001 0.005 240 Dihedral : 4.310 10.237 185 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.43 % Allowed : 22.14 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.54), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.002 0.001 TYR B 10 PHE 0.007 0.001 PHE E 20 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 1385) covalent geometry : angle 0.65735 ( 1855) hydrogen bonds : bond 0.02416 ( 40) hydrogen bonds : angle 5.46558 ( 120) *********************** 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 44 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.033 Fit side-chains REVERT: B 22 GLU cc_start: 0.8789 (tt0) cc_final: 0.8410 (tt0) REVERT: C 13 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.5981 (m-70) REVERT: E 23 ASP cc_start: 0.9252 (t0) cc_final: 0.8922 (t0) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.0408 time to fit residues: 1.9826 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 : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 13 HIS 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 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.106547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.092162 restraints weight = 2263.574| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.40 r_work: 0.3565 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1385 Z= 0.116 Angle : 0.662 8.306 1855 Z= 0.315 Chirality : 0.051 0.130 200 Planarity : 0.001 0.005 240 Dihedral : 4.223 10.233 185 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.71 % Allowed : 22.86 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.54), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 5 TYR 0.003 0.001 TYR C 10 PHE 0.008 0.001 PHE E 20 HIS 0.001 0.000 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 1385) covalent geometry : angle 0.66172 ( 1855) hydrogen bonds : bond 0.02495 ( 40) hydrogen bonds : angle 5.45529 ( 120) ********************** 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 41 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.056 Fit side-chains REVERT: B 22 GLU cc_start: 0.8790 (tt0) cc_final: 0.8327 (tt0) REVERT: C 13 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6030 (m-70) REVERT: E 23 ASP cc_start: 0.9265 (t0) cc_final: 0.8962 (t0) outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.0453 time to fit residues: 2.1153 Evaluate side-chains 38 residues out of total 140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 13 HIS 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 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.103388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.088940 restraints weight = 2340.731| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.43 r_work: 0.3511 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5656 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= 0.163 Angle : 0.680 8.257 1855 Z= 0.330 Chirality : 0.051 0.129 200 Planarity : 0.002 0.006 240 Dihedral : 4.387 11.063 185 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.14 % Allowed : 21.43 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.55), residues: 170 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.005 0.001 TYR B 10 PHE 0.009 0.002 PHE B 20 HIS 0.002 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 1385) covalent geometry : angle 0.68003 ( 1855) hydrogen bonds : bond 0.02896 ( 40) hydrogen bonds : angle 5.69665 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 562.01 seconds wall clock time: 10 minutes 50.16 seconds (650.16 seconds total)