Starting phenix.real_space_refine on Wed Mar 5 14:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c1d_30269/03_2025/7c1d_30269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c1d_30269/03_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_30269/03_2025/7c1d_30269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2025/7c1d_30269.map" model { file = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2025/7c1d_30269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_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-5624/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: 1.04, per 1000 atoms: 0.51 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: 0.71 Conformation dependent library (CDL) restraints added in 564.3 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: 0.14 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: 0.80 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- 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 : 0.191 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: 0.1219 time to fit residues: 10.8086 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 : 0.211 ------------------------------------------------------------------------------- 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 : 0.212 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: 0.0818 time to fit residues: 6.0787 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 : 0.215 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 9.9990 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: 9.9990 chunk 2 optimal weight: 0.6980 overall best weight: 4.8986 ------------------------------------------------------------------------------- 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 = 0.4841 r_free = 0.4841 target = 0.178465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.119620 restraints weight = 2515.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.121308 restraints weight = 1928.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.122349 restraints weight = 1651.872| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2040 Z= 0.304 Angle : 0.755 4.505 2766 Z= 0.443 Chirality : 0.059 0.168 366 Planarity : 0.004 0.019 354 Dihedral : 6.121 21.459 300 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.27 % Favored : 69.73 % Rotamer: Outliers : 13.54 % Allowed : 11.98 % 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: -5.67 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.044 0.011 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 71 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.8135 (mttt) cc_final: 0.7897 (mttp) REVERT: A 72 THR cc_start: 0.8589 (m) cc_final: 0.8297 (m) REVERT: C 64 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.9130 (p) REVERT: D 58 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7847 (tttt) REVERT: D 61 GLU cc_start: 0.3987 (OUTLIER) cc_final: 0.2894 (pm20) outliers start: 26 outliers final: 23 residues processed: 59 average time/residue: 0.0779 time to fit residues: 5.8396 Evaluate side-chains 68 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 52 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: 0.6980 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.0970 chunk 25 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 chunk 3 optimal weight: 0.7980 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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 = 0.5404 r_free = 0.5404 target = 0.343000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5284 r_free = 0.5284 target = 0.253452 restraints weight = 2533.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.252765 restraints weight = 4906.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.250669 restraints weight = 4331.073| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2040 Z= 0.124 Angle : 0.548 4.026 2766 Z= 0.316 Chirality : 0.051 0.151 366 Planarity : 0.002 0.015 354 Dihedral : 4.784 17.241 300 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Rotamer: Outliers : 10.94 % Allowed : 15.62 % 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: -5.34 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.016 0.004 PHE E 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 69 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.8223 (mttt) cc_final: 0.8002 (mttp) REVERT: A 72 THR cc_start: 0.8473 (m) cc_final: 0.8238 (m) REVERT: B 92 THR cc_start: 0.8611 (m) cc_final: 0.8255 (p) REVERT: C 64 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9085 (p) REVERT: C 83 GLU cc_start: 0.8458 (mp0) cc_final: 0.8037 (mp0) REVERT: D 58 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7188 (tttt) outliers start: 21 outliers final: 19 residues processed: 56 average time/residue: 0.0734 time to fit residues: 5.5001 Evaluate side-chains 63 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL 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 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 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5483 r_free = 0.5483 target = 0.355052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.262075 restraints weight = 2573.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5403 r_free = 0.5403 target = 0.260023 restraints weight = 5675.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5414 r_free = 0.5414 target = 0.260334 restraints weight = 5663.085| |-----------------------------------------------------------------------------| r_work (final): 0.5322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2040 Z= 0.109 Angle : 0.537 4.528 2766 Z= 0.304 Chirality : 0.049 0.147 366 Planarity : 0.002 0.016 354 Dihedral : 4.218 16.026 300 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 10.94 % Allowed : 13.54 % Favored : 75.52 % 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: -5.02 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.008 0.002 PHE F 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 63 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.223 Fit side-chains REVERT: E 57 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6608 (tm-30) REVERT: E 60 LYS cc_start: 0.8247 (mttt) cc_final: 0.8014 (mttp) REVERT: A 72 THR cc_start: 0.8604 (m) cc_final: 0.7951 (m) REVERT: B 92 THR cc_start: 0.8365 (m) cc_final: 0.8049 (p) REVERT: F 61 GLU cc_start: 0.7899 (tp30) cc_final: 0.7664 (tt0) REVERT: D 58 LYS cc_start: 0.7530 (mtpt) cc_final: 0.6756 (tttt) REVERT: D 61 GLU cc_start: 0.4913 (OUTLIER) cc_final: 0.3596 (pm20) outliers start: 21 outliers final: 16 residues processed: 54 average time/residue: 0.0896 time to fit residues: 6.0697 Evaluate side-chains 60 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.0270 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 = 0.334353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.242085 restraints weight = 2541.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.236278 restraints weight = 4881.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.231339 restraints weight = 6129.621| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2040 Z= 0.214 Angle : 0.647 4.601 2766 Z= 0.373 Chirality : 0.053 0.157 366 Planarity : 0.003 0.017 354 Dihedral : 5.150 18.538 300 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Rotamer: Outliers : 10.42 % Allowed : 13.54 % 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: -5.19 (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 A 50 PHE 0.028 0.008 PHE F 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 66 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7561 (tttt) REVERT: D 61 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.3355 (pm20) outliers start: 20 outliers final: 18 residues processed: 55 average time/residue: 0.0878 time to fit residues: 6.0521 Evaluate side-chains 62 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.5312 r_free = 0.5312 target = 0.333713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5228 r_free = 0.5228 target = 0.253126 restraints weight = 2578.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.253484 restraints weight = 5817.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.253259 restraints weight = 6082.538| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2040 Z= 0.255 Angle : 0.700 4.768 2766 Z= 0.408 Chirality : 0.056 0.162 366 Planarity : 0.004 0.017 354 Dihedral : 5.495 19.913 300 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.27 % Favored : 69.73 % 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: -5.36 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.035 0.009 PHE E 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 66 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8694 (m) cc_final: 0.8420 (m) REVERT: D 61 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.4041 (pm20) outliers start: 20 outliers final: 19 residues processed: 55 average time/residue: 0.0761 time to fit residues: 5.4015 Evaluate side-chains 65 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.5410 r_free = 0.5410 target = 0.294399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 216)---------------| | r_work = 0.5295 r_free = 0.5295 target = 0.228628 restraints weight = 2486.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.228607 restraints weight = 4678.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.226121 restraints weight = 3908.326| |-----------------------------------------------------------------------------| r_work (final): 0.4891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2040 Z= 0.199 Angle : 0.650 5.326 2766 Z= 0.374 Chirality : 0.053 0.160 366 Planarity : 0.003 0.018 354 Dihedral : 5.085 18.167 300 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.17 % Favored : 74.83 % Rotamer: Outliers : 9.90 % Allowed : 16.15 % Favored : 73.96 % 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: -5.21 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.30), 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 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 64 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8680 (m) cc_final: 0.8380 (m) REVERT: D 61 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.3949 (pm20) outliers start: 19 outliers final: 18 residues processed: 55 average time/residue: 0.0707 time to fit residues: 5.0423 Evaluate side-chains 62 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 61 GLU Chi-restraints excluded: chain D residue 64 THR 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: 7.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.5327 r_free = 0.5327 target = 0.336906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.248107 restraints weight = 2669.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.243579 restraints weight = 5553.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.242453 restraints weight = 5987.814| |-----------------------------------------------------------------------------| r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2040 Z= 0.215 Angle : 0.696 7.441 2766 Z= 0.398 Chirality : 0.054 0.161 366 Planarity : 0.003 0.019 354 Dihedral : 5.231 19.262 300 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.23 % Favored : 71.77 % Rotamer: Outliers : 9.90 % Allowed : 18.23 % Favored : 71.88 % 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: -5.20 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (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 *********************** 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 62 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.188 Fit side-chains REVERT: A 72 THR cc_start: 0.8653 (m) cc_final: 0.8355 (m) REVERT: F 61 GLU cc_start: 0.7923 (tp30) cc_final: 0.7648 (tt0) REVERT: D 61 GLU cc_start: 0.5351 (OUTLIER) cc_final: 0.3955 (pm20) outliers start: 19 outliers final: 18 residues processed: 53 average time/residue: 0.0721 time to fit residues: 4.9833 Evaluate side-chains 62 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 61 GLU Chi-restraints excluded: chain D residue 64 THR 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: 7.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.0770 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- 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 = 0.5393 r_free = 0.5393 target = 0.347249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.260049 restraints weight = 2535.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.257201 restraints weight = 4864.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.249504 restraints weight = 4981.256| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2040 Z= 0.128 Angle : 0.607 6.320 2766 Z= 0.343 Chirality : 0.050 0.151 366 Planarity : 0.003 0.020 354 Dihedral : 4.399 16.953 300 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % Rotamer: Outliers : 9.90 % Allowed : 18.75 % 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: -4.93 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.013 0.003 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 68 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.213 Fit side-chains REVERT: A 72 THR cc_start: 0.8514 (m) cc_final: 0.8254 (m) REVERT: B 92 THR cc_start: 0.8372 (m) cc_final: 0.7950 (p) REVERT: F 61 GLU cc_start: 0.7900 (tp30) cc_final: 0.7623 (tt0) REVERT: D 61 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.3760 (pm20) outliers start: 19 outliers final: 16 residues processed: 58 average time/residue: 0.0679 time to fit residues: 5.1948 Evaluate side-chains 65 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 0.0770 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5381 r_free = 0.5381 target = 0.345972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.265626 restraints weight = 2579.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.259373 restraints weight = 5022.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.255646 restraints weight = 5331.549| |-----------------------------------------------------------------------------| r_work (final): 0.4788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2040 Z= 0.150 Angle : 0.643 6.432 2766 Z= 0.362 Chirality : 0.050 0.153 366 Planarity : 0.003 0.020 354 Dihedral : 4.577 17.532 300 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.45 % Favored : 77.55 % 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: -4.84 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.017 0.004 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1070.72 seconds wall clock time: 19 minutes 26.41 seconds (1166.41 seconds total)