Starting phenix.real_space_refine on Mon Feb 10 19:53:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.map" model { file = "/net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c1d_30269/02_2025/7c1d_30269.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1254 2.51 5 N 360 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2034 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 0.91, per 1000 atoms: 0.45 Number of scatterers: 2034 At special positions: 0 Unit cell: (105.768, 61.02, 33.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 360 7.00 C 1254 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: 0.84 Conformation dependent library (CDL) restraints added in 275.0 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.602A pdb=" N ALA E 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.585A pdb=" N ALA F 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.02 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 372 1.29 - 1.36: 336 1.36 - 1.42: 54 1.42 - 1.48: 348 1.48 - 1.55: 930 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL F 66 " pdb=" CG2 VAL F 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL E 66 " pdb=" CG2 VAL E 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL D 66 " pdb=" CG2 VAL D 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CB VAL C 66 " pdb=" CG2 VAL C 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CB VAL B 66 " pdb=" CG2 VAL B 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.83e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 2431 1.02 - 2.04: 286 2.04 - 3.07: 37 3.07 - 4.09: 6 4.09 - 5.11: 6 Bond angle restraints: 2766 Sorted by residual: angle pdb=" N GLY F 51 " pdb=" CA GLY F 51 " pdb=" C GLY F 51 " ideal model delta sigma weight residual 110.18 115.29 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY A 51 " pdb=" CA GLY A 51 " pdb=" C GLY A 51 " ideal model delta sigma weight residual 110.18 115.28 -5.10 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY D 51 " pdb=" CA GLY D 51 " pdb=" C GLY D 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY E 51 " pdb=" CA GLY E 51 " pdb=" C GLY E 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY B 51 " pdb=" CA GLY B 51 " pdb=" C GLY B 51 " ideal model delta sigma weight residual 110.18 115.22 -5.04 1.56e+00 4.11e-01 1.04e+01 ... (remaining 2761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 1074 16.53 - 33.05: 78 33.05 - 49.58: 18 49.58 - 66.11: 0 66.11 - 82.63: 6 Dihedral angle restraints: 1176 sinusoidal: 360 harmonic: 816 Sorted by residual: dihedral pdb=" CA ILE E 88 " pdb=" C ILE E 88 " pdb=" N ALA E 89 " pdb=" CA ALA E 89 " ideal model delta harmonic sigma weight residual 180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " pdb=" CA ALA A 89 " ideal model delta harmonic sigma weight residual 180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE C 88 " pdb=" C ILE C 88 " pdb=" N ALA C 89 " pdb=" CA ALA C 89 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 160 0.026 - 0.053: 93 0.053 - 0.079: 55 0.079 - 0.106: 28 0.106 - 0.132: 30 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL D 95 " pdb=" N VAL D 95 " pdb=" C VAL D 95 " pdb=" CB VAL D 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 363 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.008 2.00e-02 2.50e+03 6.91e-03 8.35e-01 pdb=" CG PHE D 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.009 2.00e-02 2.50e+03 6.85e-03 8.22e-01 pdb=" CG PHE C 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.008 2.00e-02 2.50e+03 6.81e-03 8.12e-01 pdb=" CG PHE B 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 852 2.87 - 3.38: 1890 3.38 - 3.89: 3196 3.89 - 4.39: 3053 4.39 - 4.90: 6398 Nonbonded interactions: 15389 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" OG SER A 87 " model vdw 2.367 3.040 nonbonded pdb=" O GLY C 84 " pdb=" OG SER C 87 " model vdw 2.367 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OG SER B 87 " model vdw 2.368 3.040 nonbonded pdb=" O GLY F 84 " pdb=" OG SER F 87 " model vdw 2.368 3.040 nonbonded pdb=" O GLY D 84 " pdb=" OG SER D 87 " model vdw 2.368 3.040 ... (remaining 15384 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 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.460 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- 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 : 0.004 0.030 2040 Z= 0.178 Angle : 0.709 5.111 2766 Z= 0.456 Chirality : 0.054 0.132 366 Planarity : 0.003 0.008 354 Dihedral : 13.995 82.631 660 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.41 % Favored : 79.59 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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: -6.46 (0.32), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.92 (0.25), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS F 50 PHE 0.016 0.004 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.7901 (mttt) cc_final: 0.7668 (mttp) REVERT: E 61 GLU cc_start: 0.8046 (tp30) cc_final: 0.7698 (tp30) REVERT: E 83 GLU cc_start: 0.8173 (mp0) cc_final: 0.7947 (mp0) REVERT: A 72 THR cc_start: 0.8327 (m) cc_final: 0.8093 (m) REVERT: B 83 GLU cc_start: 0.8800 (mp0) cc_final: 0.8487 (mp0) REVERT: B 92 THR cc_start: 0.8360 (m) cc_final: 0.7980 (p) REVERT: C 64 THR cc_start: 0.8989 (t) cc_final: 0.8709 (t) REVERT: C 83 GLU cc_start: 0.8624 (mp0) cc_final: 0.8400 (mp0) REVERT: D 83 GLU cc_start: 0.8555 (mp0) cc_final: 0.8146 (mp0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1235 time to fit residues: 10.9098 Evaluate side-chains 56 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 20.0000 chunk 22 optimal weight: 0.0870 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5374 r_free = 0.5374 target = 0.338368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.247596 restraints weight = 2535.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.245575 restraints weight = 5350.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.245006 restraints weight = 5203.196| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2040 Z= 0.166 Angle : 0.590 4.089 2766 Z= 0.342 Chirality : 0.053 0.159 366 Planarity : 0.003 0.012 354 Dihedral : 5.040 17.764 300 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.79 % Favored : 77.21 % Rotamer: Outliers : 10.94 % Allowed : 10.94 % Favored : 78.12 % 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: -5.78 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.024 0.006 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.223 Fit side-chains REVERT: E 60 LYS cc_start: 0.8116 (mttt) cc_final: 0.7904 (mttp) REVERT: E 61 GLU cc_start: 0.8218 (tp30) cc_final: 0.7968 (tp30) REVERT: A 72 THR cc_start: 0.8452 (m) cc_final: 0.8202 (m) REVERT: B 92 THR cc_start: 0.8565 (m) cc_final: 0.8264 (p) REVERT: C 64 THR cc_start: 0.9364 (t) cc_final: 0.9129 (t) REVERT: C 83 GLU cc_start: 0.8681 (mp0) cc_final: 0.8450 (mp0) outliers start: 21 outliers final: 20 residues processed: 59 average time/residue: 0.0816 time to fit residues: 6.0475 Evaluate side-chains 64 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.193321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.136241 restraints weight = 2312.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.134660 restraints weight = 1997.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.134914 restraints weight = 2251.192| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2040 Z= 0.227 Angle : 0.654 4.316 2766 Z= 0.381 Chirality : 0.055 0.161 366 Planarity : 0.003 0.014 354 Dihedral : 5.479 18.963 300 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Rotamer: Outliers : 13.54 % Allowed : 10.42 % Favored : 76.04 % 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: -5.57 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.032 0.008 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.8138 (mttt) cc_final: 0.7896 (mttp) REVERT: E 61 GLU cc_start: 0.8029 (tp30) cc_final: 0.7822 (tp30) REVERT: A 72 THR cc_start: 0.8500 (m) cc_final: 0.8243 (m) REVERT: B 92 THR cc_start: 0.8887 (m) cc_final: 0.8445 (p) REVERT: C 64 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9103 (p) REVERT: C 83 GLU cc_start: 0.8483 (mp0) cc_final: 0.7851 (mp0) REVERT: D 58 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7972 (tttt) REVERT: D 61 GLU cc_start: 0.3702 (OUTLIER) cc_final: 0.2682 (pm20) outliers start: 26 outliers final: 22 residues processed: 57 average time/residue: 0.0743 time to fit residues: 5.4003 Evaluate side-chains 67 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.347350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.263700 restraints weight = 2526.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.261236 restraints weight = 4967.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.255173 restraints weight = 5327.778| |-----------------------------------------------------------------------------| r_work (final): 0.4735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2040 Z= 0.116 Angle : 0.512 4.004 2766 Z= 0.295 Chirality : 0.050 0.150 366 Planarity : 0.002 0.015 354 Dihedral : 4.484 16.479 300 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.99 % Favored : 84.01 % Rotamer: Outliers : 10.42 % Allowed : 14.58 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.014 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.8245 (mttt) cc_final: 0.8016 (mttp) REVERT: A 72 THR cc_start: 0.8554 (m) cc_final: 0.8300 (m) REVERT: D 58 LYS cc_start: 0.7639 (mtpt) cc_final: 0.6947 (tttt) outliers start: 20 outliers final: 17 residues processed: 52 average time/residue: 0.0814 time to fit residues: 5.4022 Evaluate side-chains 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.333491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.246474 restraints weight = 2599.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.241226 restraints weight = 5068.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.237679 restraints weight = 5286.292| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2040 Z= 0.228 Angle : 0.649 4.490 2766 Z= 0.378 Chirality : 0.054 0.160 366 Planarity : 0.003 0.015 354 Dihedral : 5.379 19.236 300 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.21 % Favored : 72.79 % Rotamer: Outliers : 10.94 % Allowed : 14.58 % Favored : 74.48 % 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: -5.37 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.030 0.008 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.8228 (mttt) cc_final: 0.8017 (mttp) REVERT: A 72 THR cc_start: 0.8523 (m) cc_final: 0.8264 (m) REVERT: D 58 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7348 (tttt) REVERT: D 61 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3159 (pm20) outliers start: 21 outliers final: 20 residues processed: 56 average time/residue: 0.0797 time to fit residues: 5.6576 Evaluate side-chains 67 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.284539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.233373 restraints weight = 2458.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.231877 restraints weight = 4762.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.231081 restraints weight = 5145.795| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2040 Z= 0.304 Angle : 0.743 4.594 2766 Z= 0.438 Chirality : 0.059 0.190 366 Planarity : 0.004 0.018 354 Dihedral : 5.858 20.471 300 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.99 % Favored : 67.01 % Rotamer: Outliers : 10.94 % Allowed : 16.15 % Favored : 72.92 % 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: -5.56 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.041 0.011 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8497 (m) cc_final: 0.8271 (m) REVERT: D 61 GLU cc_start: 0.4771 (OUTLIER) cc_final: 0.3437 (pm20) outliers start: 21 outliers final: 20 residues processed: 59 average time/residue: 0.0820 time to fit residues: 6.1868 Evaluate side-chains 66 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.353548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.262882 restraints weight = 2553.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.258267 restraints weight = 5250.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.257986 restraints weight = 5451.444| |-----------------------------------------------------------------------------| r_work (final): 0.5296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2040 Z= 0.112 Angle : 0.564 5.103 2766 Z= 0.321 Chirality : 0.050 0.156 366 Planarity : 0.003 0.017 354 Dihedral : 4.320 16.133 300 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 8.85 % Allowed : 17.71 % Favored : 73.44 % 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: -5.16 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8701 (m) cc_final: 0.8445 (m) REVERT: B 64 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8859 (p) REVERT: F 61 GLU cc_start: 0.7914 (tp30) cc_final: 0.7645 (tt0) REVERT: D 61 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.3624 (pm20) outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.0664 time to fit residues: 4.7363 Evaluate side-chains 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.341089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.255280 restraints weight = 2613.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.252042 restraints weight = 5587.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.249199 restraints weight = 6019.679| |-----------------------------------------------------------------------------| r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2040 Z= 0.196 Angle : 0.689 6.686 2766 Z= 0.391 Chirality : 0.053 0.165 366 Planarity : 0.003 0.019 354 Dihedral : 4.946 18.206 300 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Rotamer: Outliers : 9.38 % Allowed : 19.27 % Favored : 71.35 % 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: -5.19 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.024 0.006 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8465 (m) cc_final: 0.8208 (m) REVERT: D 61 GLU cc_start: 0.5243 (OUTLIER) cc_final: 0.3775 (pm20) outliers start: 18 outliers final: 16 residues processed: 53 average time/residue: 0.0573 time to fit residues: 4.2820 Evaluate side-chains 58 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.334751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.249388 restraints weight = 2669.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.243192 restraints weight = 5650.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.240868 restraints weight = 5992.813| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2040 Z= 0.243 Angle : 0.736 6.199 2766 Z= 0.422 Chirality : 0.056 0.181 366 Planarity : 0.004 0.020 354 Dihedral : 5.444 19.396 300 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.55 % Favored : 72.45 % Rotamer: Outliers : 8.85 % Allowed : 20.83 % Favored : 70.31 % 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: -5.31 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.030 0.008 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8498 (m) cc_final: 0.8284 (m) REVERT: D 61 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.3953 (pm20) outliers start: 17 outliers final: 16 residues processed: 50 average time/residue: 0.0636 time to fit residues: 4.3271 Evaluate side-chains 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.337501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.249099 restraints weight = 2550.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.247382 restraints weight = 5466.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5221 r_free = 0.5221 target = 0.245834 restraints weight = 4860.272| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2040 Z= 0.206 Angle : 0.693 5.629 2766 Z= 0.396 Chirality : 0.054 0.173 366 Planarity : 0.003 0.019 354 Dihedral : 5.173 18.360 300 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.49 % Favored : 75.51 % Rotamer: Outliers : 8.85 % Allowed : 20.83 % Favored : 70.31 % 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: -5.22 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.026 0.006 PHE E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8539 (m) cc_final: 0.8309 (m) REVERT: D 61 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.3828 (pm20) outliers start: 17 outliers final: 16 residues processed: 49 average time/residue: 0.0527 time to fit residues: 3.7664 Evaluate side-chains 56 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.336952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.248226 restraints weight = 2597.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.243491 restraints weight = 5469.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.242213 restraints weight = 5940.253| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2040 Z= 0.217 Angle : 0.701 5.252 2766 Z= 0.403 Chirality : 0.055 0.171 366 Planarity : 0.003 0.020 354 Dihedral : 5.295 19.287 300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.51 % Favored : 74.49 % Rotamer: Outliers : 9.38 % Allowed : 20.31 % Favored : 70.31 % 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: -5.19 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.028 0.007 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1032.63 seconds wall clock time: 19 minutes 11.16 seconds (1151.16 seconds total)