Starting phenix.real_space_refine on Wed Mar 5 15:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot3_17167/03_2025/8ot3_17167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot3_17167/03_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_17167/03_2025/8ot3_17167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot3_17167/03_2025/8ot3_17167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot3_17167/03_2025/8ot3_17167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot3_17167/03_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-5624/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: 1.34, per 1000 atoms: 0.54 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: 0.53 Conformation dependent library (CDL) restraints added in 298.0 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: 0.37 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: 0.52 Time building geometry restraints manager: 0.65 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: 0.680 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: 0.020 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- 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= 0.948 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 *********************** 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 : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.5566 time to fit residues: 54.6650 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 : 0.238 ------------------------------------------------------------------------------- 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: 0.7597 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= 0.194 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 *********************** 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 : 0.283 Fit side-chains REVERT: C 22 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7529 (tm-30) REVERT: J 13 HIS cc_start: 0.6332 (m90) cc_final: 0.6104 (m90) REVERT: J 22 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7435 (tm-30) REVERT: L 13 HIS cc_start: 0.6819 (m90) cc_final: 0.6490 (m90) REVERT: L 22 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7641 (tm-30) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.6343 time to fit residues: 35.0812 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: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.116242 restraints weight = 3630.285| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.55 r_work: 0.4134 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4015 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 0.015 2496 Z= 0.195 Angle : 0.615 6.595 3336 Z= 0.327 Chirality : 0.051 0.120 384 Planarity : 0.002 0.011 420 Dihedral : 3.997 10.104 324 Min Nonbonded Distance : 2.637 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: -3.87 (0.24), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 14 PHE 0.012 0.002 PHE J 20 *********************** 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 46 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.272 Fit side-chains REVERT: J 22 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7394 (tm-30) REVERT: L 22 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7680 (tm-30) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.8340 time to fit residues: 37.1409 Evaluate side-chains 44 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.130209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.112191 restraints weight = 3668.332| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.51 r_work: 0.4078 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 2496 Z= 0.375 Angle : 0.714 5.876 3336 Z= 0.382 Chirality : 0.051 0.119 384 Planarity : 0.003 0.011 420 Dihedral : 4.586 10.988 324 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.44 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: -4.18 (0.22), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.17), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS B 14 PHE 0.017 0.003 PHE G 20 *********************** 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 50 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.245 Fit side-chains REVERT: A 13 HIS cc_start: 0.6887 (m90) cc_final: 0.6168 (m90) REVERT: J 22 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7640 (tm-30) REVERT: L 22 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7734 (tm-30) outliers start: 11 outliers final: 9 residues processed: 48 average time/residue: 0.7961 time to fit residues: 39.5830 Evaluate side-chains 47 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 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 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: 4.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.0040 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.114429 restraints weight = 3706.961| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.60 r_work: 0.4110 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2496 Z= 0.250 Angle : 0.642 8.896 3336 Z= 0.336 Chirality : 0.051 0.126 384 Planarity : 0.002 0.010 420 Dihedral : 4.251 10.081 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.37 % Allowed : 21.43 % 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: -4.02 (0.23), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS C 14 PHE 0.013 0.002 PHE G 20 *********************** 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 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.257 Fit side-chains REVERT: L 22 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.8197 time to fit residues: 34.0341 Evaluate side-chains 38 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 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 = 0.4506 r_free = 0.4506 target = 0.134380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.116051 restraints weight = 3893.045| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.73 r_work: 0.4134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2496 Z= 0.162 Angle : 0.573 8.015 3336 Z= 0.297 Chirality : 0.051 0.122 384 Planarity : 0.002 0.010 420 Dihedral : 3.997 9.807 324 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 22.62 % 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: -3.66 (0.26), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 14 PHE 0.010 0.002 PHE G 20 *********************** 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 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.243 Fit side-chains REVERT: L 22 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7537 (tm-30) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.9202 time to fit residues: 36.1983 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.114081 restraints weight = 3704.329| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.61 r_work: 0.4115 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5255 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= 0.215 Angle : 0.604 7.434 3336 Z= 0.314 Chirality : 0.050 0.123 384 Planarity : 0.002 0.014 420 Dihedral : 4.196 9.655 324 Min Nonbonded Distance : 2.514 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: -3.55 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.011 0.002 PHE I 20 *********************** 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 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.281 Fit side-chains REVERT: L 22 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7694 (tm-30) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.8233 time to fit residues: 32.4335 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.132964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.114805 restraints weight = 3934.943| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.68 r_work: 0.4129 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5349 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= 0.189 Angle : 0.599 7.111 3336 Z= 0.311 Chirality : 0.050 0.122 384 Planarity : 0.002 0.017 420 Dihedral : 4.117 9.563 324 Min Nonbonded Distance : 2.524 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: -3.38 (0.30), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.010 0.002 PHE I 20 *********************** 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 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.247 Fit side-chains REVERT: L 22 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7550 (tm-30) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.8022 time to fit residues: 32.4563 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.116569 restraints weight = 3891.146| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.71 r_work: 0.4145 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2496 Z= 0.170 Angle : 0.611 6.939 3336 Z= 0.316 Chirality : 0.050 0.121 384 Planarity : 0.002 0.022 420 Dihedral : 4.027 9.791 324 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 22.22 % 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: -3.25 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 14 PHE 0.009 0.001 PHE I 20 *********************** 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 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.271 Fit side-chains REVERT: L 22 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7557 (tm-30) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.8459 time to fit residues: 33.3108 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.131843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.113498 restraints weight = 3874.489| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.66 r_work: 0.4100 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2496 Z= 0.276 Angle : 0.707 7.444 3336 Z= 0.369 Chirality : 0.050 0.124 384 Planarity : 0.002 0.005 420 Dihedral : 4.345 9.848 324 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 21.83 % 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: -3.44 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 14 PHE 0.012 0.002 PHE I 20 ********************** 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 44 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.252 Fit side-chains REVERT: L 22 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7592 (tm-30) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 0.8310 time to fit residues: 35.2819 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 : 0.280 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.115706 restraints weight = 3904.090| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.66 r_work: 0.4147 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2496 Z= 0.181 Angle : 0.639 6.775 3336 Z= 0.332 Chirality : 0.050 0.121 384 Planarity : 0.003 0.029 420 Dihedral : 4.074 9.418 324 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.25 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: -3.28 (0.32), 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 0.005 0.001 HIS C 14 PHE 0.009 0.001 PHE D 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.51 seconds wall clock time: 43 minutes 46.05 seconds (2626.05 seconds total)