Starting phenix.real_space_refine on Fri May 9 14:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot3_17167/05_2025/8ot3_17167.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1596 2.51 5 N 432 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.25, per 1000 atoms: 0.51 Number of scatterers: 2460 At special positions: 0 Unit cell: (92.466, 73.786, 42.964, 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 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.44 Conformation dependent library (CDL) restraints added in 229.1 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 17 " --> pdb=" O VAL K 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP C 23 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP E 23 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP G 23 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP I 23 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP K 23 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 17 " --> pdb=" O VAL L 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP D 23 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP F 23 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP H 23 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP J 23 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP L 23 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 32 30 hydrogen bonds defined for protein. 90 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: 0.49 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 408 1.29 - 1.42: 612 1.42 - 1.55: 1452 1.55 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" C ILE K 32 " pdb=" O ILE K 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE G 32 " pdb=" O ILE G 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE D 32 " pdb=" O ILE D 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE L 32 " pdb=" O ILE L 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE J 32 " pdb=" O ILE J 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 2101 1.95 - 3.90: 867 3.90 - 5.85: 356 5.85 - 7.80: 0 7.80 - 9.75: 12 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY I 38 " pdb=" C GLY I 38 " pdb=" O GLY I 38 " ideal model delta sigma weight residual 122.23 118.44 3.79 6.90e-01 2.10e+00 3.02e+01 angle pdb=" CA GLY B 38 " pdb=" C GLY B 38 " pdb=" O GLY B 38 " ideal model delta sigma weight residual 122.23 118.47 3.76 6.90e-01 2.10e+00 2.96e+01 angle pdb=" CA GLY A 38 " pdb=" C GLY A 38 " pdb=" O GLY A 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY J 38 " pdb=" C GLY J 38 " pdb=" O GLY J 38 " ideal model delta sigma weight residual 122.23 118.49 3.74 6.90e-01 2.10e+00 2.94e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1272 16.52 - 33.03: 72 33.03 - 49.55: 36 49.55 - 66.07: 0 66.07 - 82.58: 12 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA ILE F 32 " pdb=" CB ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CD1 ILE F 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE L 32 " pdb=" CB ILE L 32 " pdb=" CG1 ILE L 32 " pdb=" CD1 ILE L 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE J 32 " pdb=" CB ILE J 32 " pdb=" CG1 ILE J 32 " pdb=" CD1 ILE J 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.47 48.53 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 60 0.045 - 0.091: 72 0.091 - 0.136: 108 0.136 - 0.181: 65 0.181 - 0.227: 79 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE I 32 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE I 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE C 32 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE C 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 32 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE H 32 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE H 32 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY H 33 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1370 3.03 - 3.50: 2330 3.50 - 3.96: 3720 3.96 - 4.43: 4345 4.43 - 4.90: 8804 Nonbonded interactions: 20569 Sorted by model distance: nonbonded pdb=" N VAL B 36 " pdb=" O VAL B 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL D 36 " pdb=" O VAL D 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL A 36 " pdb=" O VAL A 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL L 36 " pdb=" O VAL L 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL I 36 " pdb=" O VAL I 36 " model vdw 2.559 2.496 ... (remaining 20564 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.070 Find NCS groups from input model: 0.040 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.014 0.075 2496 Z= 1.104 Angle : 2.331 9.747 3336 Z= 1.679 Chirality : 0.131 0.227 384 Planarity : 0.010 0.032 420 Dihedral : 16.882 82.580 840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 14 PHE 0.008 0.002 PHE K 20 Details of bonding type rmsd hydrogen bonds : bond 0.23922 ( 30) hydrogen bonds : angle 11.18109 ( 90) covalent geometry : bond 0.01419 ( 2496) covalent geometry : angle 2.33059 ( 3336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5142 time to fit residues: 50.4538 Evaluate side-chains 88 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 C 14 HIS E 14 HIS G 14 HIS I 14 HIS J 14 HIS K 14 HIS L 14 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.136641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.119745 restraints weight = 3583.605| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.47 r_work: 0.4184 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2496 Z= 0.147 Angle : 0.702 7.756 3336 Z= 0.379 Chirality : 0.052 0.116 384 Planarity : 0.002 0.013 420 Dihedral : 4.129 10.404 324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 21.83 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.24), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS C 14 PHE 0.012 0.002 PHE H 20 Details of bonding type rmsd hydrogen bonds : bond 0.01843 ( 30) hydrogen bonds : angle 3.51460 ( 90) covalent geometry : bond 0.00290 ( 2496) covalent geometry : angle 0.70227 ( 3336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.274 Fit side-chains REVERT: C 22 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7530 (tm-30) REVERT: J 13 HIS cc_start: 0.6332 (m90) cc_final: 0.6104 (m90) REVERT: J 22 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7435 (tm-30) REVERT: L 13 HIS cc_start: 0.6819 (m90) cc_final: 0.6489 (m90) REVERT: L 22 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.6569 time to fit residues: 36.2972 Evaluate side-chains 48 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 C 14 HIS G 14 HIS K 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.133627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.115994 restraints weight = 3640.199| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.57 r_work: 0.4126 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.138 Angle : 0.624 6.738 3336 Z= 0.332 Chirality : 0.051 0.120 384 Planarity : 0.002 0.011 420 Dihedral : 4.031 10.167 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 23.41 % Favored : 73.81 % 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: -3.89 (0.24), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 14 PHE 0.013 0.002 PHE E 20 Details of bonding type rmsd hydrogen bonds : bond 0.01985 ( 30) hydrogen bonds : angle 3.64806 ( 90) covalent geometry : bond 0.00305 ( 2496) covalent geometry : angle 0.62370 ( 3336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.267 Fit side-chains REVERT: J 22 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7384 (tm-30) REVERT: L 22 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.8561 time to fit residues: 37.2386 Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS K 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.133862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.115017 restraints weight = 3726.597| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.67 r_work: 0.4139 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 2496 Z= 0.282 Angle : 0.762 6.031 3336 Z= 0.409 Chirality : 0.052 0.120 384 Planarity : 0.003 0.011 420 Dihedral : 4.729 10.990 324 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.37 % Allowed : 21.03 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.21), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.16), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS K 14 PHE 0.018 0.004 PHE G 20 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 30) hydrogen bonds : angle 4.32195 ( 90) covalent geometry : bond 0.00655 ( 2496) covalent geometry : angle 0.76191 ( 3336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.332 Fit side-chains REVERT: J 22 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7594 (tm-30) REVERT: L 22 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7722 (tm-30) outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.8567 time to fit residues: 45.1616 Evaluate side-chains 48 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 14 HIS K 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.135649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.117344 restraints weight = 3941.319| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.69 r_work: 0.4144 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2496 Z= 0.104 Angle : 0.584 9.208 3336 Z= 0.301 Chirality : 0.052 0.126 384 Planarity : 0.001 0.010 420 Dihedral : 3.963 10.105 324 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 23.02 % Favored : 73.81 % 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: -3.85 (0.24), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 14 PHE 0.010 0.002 PHE G 20 Details of bonding type rmsd hydrogen bonds : bond 0.01801 ( 30) hydrogen bonds : angle 3.50612 ( 90) covalent geometry : bond 0.00216 ( 2496) covalent geometry : angle 0.58392 ( 3336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.276 Fit side-chains REVERT: A 22 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 35 MET cc_start: 0.7562 (mtt) cc_final: 0.7254 (mtt) REVERT: L 22 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7507 (tm-30) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.9650 time to fit residues: 35.8896 Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.132893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.114983 restraints weight = 3640.374| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.59 r_work: 0.4143 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2496 Z= 0.121 Angle : 0.587 8.167 3336 Z= 0.303 Chirality : 0.050 0.123 384 Planarity : 0.002 0.010 420 Dihedral : 4.041 9.926 324 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 23.41 % Favored : 73.02 % 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: -3.58 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 14 PHE 0.010 0.002 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.01721 ( 30) hydrogen bonds : angle 3.65696 ( 90) covalent geometry : bond 0.00271 ( 2496) covalent geometry : angle 0.58672 ( 3336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.270 Fit side-chains REVERT: B 23 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8104 (t0) REVERT: L 22 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7573 (tm-30) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.8101 time to fit residues: 32.7836 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.130739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.112568 restraints weight = 3723.777| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.58 r_work: 0.4096 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3974 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2496 Z= 0.178 Angle : 0.637 7.637 3336 Z= 0.333 Chirality : 0.050 0.124 384 Planarity : 0.002 0.013 420 Dihedral : 4.330 10.115 324 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 21.03 % Favored : 74.21 % 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: -3.68 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.013 0.002 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.02290 ( 30) hydrogen bonds : angle 3.87817 ( 90) covalent geometry : bond 0.00410 ( 2496) covalent geometry : angle 0.63653 ( 3336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.280 Fit side-chains REVERT: L 22 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7761 (tm-30) outliers start: 12 outliers final: 9 residues processed: 41 average time/residue: 0.7421 time to fit residues: 31.6105 Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.115668 restraints weight = 3970.251| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.71 r_work: 0.4120 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2496 Z= 0.126 Angle : 0.596 7.266 3336 Z= 0.310 Chirality : 0.050 0.122 384 Planarity : 0.002 0.015 420 Dihedral : 4.133 9.679 324 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 21.83 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.29), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.010 0.002 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.01873 ( 30) hydrogen bonds : angle 3.67457 ( 90) covalent geometry : bond 0.00281 ( 2496) covalent geometry : angle 0.59558 ( 3336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.289 Fit side-chains REVERT: L 22 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7517 (tm-30) outliers start: 9 outliers final: 8 residues processed: 40 average time/residue: 0.7715 time to fit residues: 32.0639 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.134200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.116378 restraints weight = 3892.685| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.66 r_work: 0.4152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2496 Z= 0.112 Angle : 0.600 7.085 3336 Z= 0.311 Chirality : 0.050 0.121 384 Planarity : 0.001 0.019 420 Dihedral : 4.015 9.569 324 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 21.83 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 14 PHE 0.008 0.001 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.01570 ( 30) hydrogen bonds : angle 3.51352 ( 90) covalent geometry : bond 0.00246 ( 2496) covalent geometry : angle 0.59971 ( 3336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.262 Fit side-chains REVERT: B 23 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7955 (t0) REVERT: L 22 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7598 (tm-30) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.7910 time to fit residues: 32.0280 Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.133617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.115387 restraints weight = 3685.185| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.64 r_work: 0.4147 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4032 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2496 Z= 0.214 Angle : 0.722 6.988 3336 Z= 0.378 Chirality : 0.050 0.124 384 Planarity : 0.003 0.026 420 Dihedral : 4.467 10.030 324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 22.22 % Favored : 73.81 % 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: -3.58 (0.30), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 14 PHE 0.014 0.003 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.02344 ( 30) hydrogen bonds : angle 3.94250 ( 90) covalent geometry : bond 0.00490 ( 2496) covalent geometry : angle 0.72166 ( 3336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.276 Fit side-chains REVERT: D 23 ASP cc_start: 0.8314 (t0) cc_final: 0.8101 (t70) REVERT: L 22 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7700 (tm-30) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.8432 time to fit residues: 34.9683 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.133015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.115119 restraints weight = 3912.382| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.66 r_work: 0.4131 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2496 Z= 0.131 Angle : 0.661 7.421 3336 Z= 0.344 Chirality : 0.050 0.125 384 Planarity : 0.002 0.028 420 Dihedral : 4.142 9.547 324 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.57 % Allowed : 22.62 % Favored : 73.81 % 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: -3.41 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 14 PHE 0.009 0.002 PHE I 20 Details of bonding type rmsd hydrogen bonds : bond 0.01816 ( 30) hydrogen bonds : angle 3.58188 ( 90) covalent geometry : bond 0.00294 ( 2496) covalent geometry : angle 0.66136 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.41 seconds wall clock time: 42 minutes 36.18 seconds (2556.18 seconds total)