Starting phenix.real_space_refine on Tue Mar 3 10:48:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_30269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_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 { model { file = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_30269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_30269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_30269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c1d_30269/03_2026/7c1d_30269.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2034 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" 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: A, B, F, C, D Time building chain proxies: 0.32, per 1000 atoms: 0.16 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: 0.16 Conformation dependent library (CDL) restraints added in 63.9 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: 0.05 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: 0.01 Time building geometry restraints manager: 0.20 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'C' selection = chain 'D' } 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: 0.580 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.440 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.260 ------------------------------------------------------------------------------- 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 : 18.63 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 PHE 0.016 0.004 PHE D 94 HIS 0.002 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2040) covalent geometry : angle 0.70941 ( 2766) *********************** 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 : 0.041 Fit side-chains revert: symmetry clash REVERT: E 60 LYS cc_start: 0.7901 (mttt) cc_final: 0.7670 (mttp) REVERT: E 61 GLU cc_start: 0.8046 (tp30) cc_final: 0.7696 (tp30) REVERT: E 83 GLU cc_start: 0.8173 (mp0) cc_final: 0.7947 (mp0) REVERT: A 72 THR cc_start: 0.8326 (m) cc_final: 0.8092 (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: 0.7979 (p) REVERT: C 64 THR cc_start: 0.8989 (t) cc_final: 0.8708 (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: 0.8145 (mp0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0321 time to fit residues: 2.8639 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 : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 overall best weight: 2.5924 ------------------------------------------------------------------------------- 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 = 0.5368 r_free = 0.5368 target = 0.336916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.248651 restraints weight = 2589.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.247841 restraints weight = 5310.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.247063 restraints weight = 4909.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.244727 restraints weight = 5245.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.243629 restraints weight = 5382.705| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2040 Z= 0.176 Angle : 0.606 4.146 2766 Z= 0.350 Chirality : 0.053 0.157 366 Planarity : 0.003 0.011 354 Dihedral : 5.131 18.076 300 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.47 % Favored : 76.53 % Rotamer: Outliers : 11.46 % Allowed : 10.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.78 (0.36), 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 PHE 0.025 0.006 PHE D 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 2040) covalent geometry : angle 0.60580 ( 2766) *********************** 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 71 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.050 Fit side-chains REVERT: E 60 LYS cc_start: 0.8129 (mttt) cc_final: 0.7919 (mttp) REVERT: E 61 GLU cc_start: 0.8200 (tp30) cc_final: 0.7956 (tp30) REVERT: A 72 THR cc_start: 0.8607 (m) cc_final: 0.8346 (m) REVERT: B 92 THR cc_start: 0.8554 (m) cc_final: 0.8168 (p) REVERT: C 64 THR cc_start: 0.9380 (t) cc_final: 0.9146 (t) REVERT: C 83 GLU cc_start: 0.8666 (mp0) cc_final: 0.8419 (mp0) outliers start: 22 outliers final: 21 residues processed: 59 average time/residue: 0.0298 time to fit residues: 2.2426 Evaluate side-chains 65 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 25 optimal weight: 0.0030 chunk 29 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 HIS ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5498 r_free = 0.5498 target = 0.353639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.262997 restraints weight = 2546.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.260645 restraints weight = 5510.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5448 r_free = 0.5448 target = 0.261518 restraints weight = 5267.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5448 r_free = 0.5448 target = 0.260255 restraints weight = 4481.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.260631 restraints weight = 4079.319| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2040 Z= 0.100 Angle : 0.507 4.034 2766 Z= 0.289 Chirality : 0.049 0.150 366 Planarity : 0.002 0.014 354 Dihedral : 4.227 15.449 300 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 9.38 % Allowed : 11.98 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.25 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE F 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 2040) covalent geometry : angle 0.50706 ( 2766) *********************** 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 60 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 72 THR cc_start: 0.8451 (m) cc_final: 0.8216 (m) REVERT: B 92 THR cc_start: 0.8286 (m) cc_final: 0.8038 (p) REVERT: D 58 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7258 (tttt) outliers start: 18 outliers final: 12 residues processed: 50 average time/residue: 0.0355 time to fit residues: 2.2677 Evaluate side-chains 49 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain A residue 52 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 C residue 52 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.5262 r_free = 0.5262 target = 0.320324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.233200 restraints weight = 2593.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.227572 restraints weight = 5335.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.224418 restraints weight = 6464.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.223573 restraints weight = 5435.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.222800 restraints weight = 5403.552| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 2040 Z= 0.356 Angle : 0.784 4.560 2766 Z= 0.463 Chirality : 0.060 0.168 366 Planarity : 0.005 0.021 354 Dihedral : 6.200 22.913 300 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 35.03 % Favored : 64.97 % Rotamer: Outliers : 10.94 % Allowed : 12.50 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.66 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.012 PHE D 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 2040) covalent geometry : angle 0.78379 ( 2766) *********************** 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 68 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7723 (tttt) REVERT: D 61 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.3286 (pm20) outliers start: 21 outliers final: 19 residues processed: 57 average time/residue: 0.0307 time to fit residues: 2.3099 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 : 0.074 ------------------------------------------------------------------------------- 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 52 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.5362 r_free = 0.5362 target = 0.337201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.246112 restraints weight = 2596.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.239123 restraints weight = 5212.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.235811 restraints weight = 6568.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.235613 restraints weight = 5979.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5277 r_free = 0.5277 target = 0.235392 restraints weight = 4459.041| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2040 Z= 0.177 Angle : 0.609 4.357 2766 Z= 0.354 Chirality : 0.053 0.160 366 Planarity : 0.003 0.016 354 Dihedral : 5.161 18.054 300 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.07 % Favored : 79.93 % Rotamer: Outliers : 10.42 % Allowed : 15.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.41 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.006 PHE E 94 HIS 0.005 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2040) covalent geometry : angle 0.60861 ( 2766) *********************** 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 61 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: B 92 THR cc_start: 0.8742 (m) cc_final: 0.8262 (p) REVERT: D 58 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7493 (tttt) REVERT: D 61 GLU cc_start: 0.4132 (OUTLIER) cc_final: 0.2993 (pm20) outliers start: 20 outliers final: 18 residues processed: 52 average time/residue: 0.0255 time to fit residues: 1.8484 Evaluate side-chains 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 B residue 72 THR 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 0 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 0.0270 chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 overall best weight: 2.2042 ------------------------------------------------------------------------------- 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 = 0.5376 r_free = 0.5376 target = 0.341149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.248311 restraints weight = 2547.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.243728 restraints weight = 5255.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.240687 restraints weight = 6324.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.240187 restraints weight = 5149.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.238761 restraints weight = 5321.150| |-----------------------------------------------------------------------------| r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2040 Z= 0.156 Angle : 0.561 4.255 2766 Z= 0.326 Chirality : 0.051 0.157 366 Planarity : 0.003 0.017 354 Dihedral : 4.874 18.615 300 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.11 % Favored : 77.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.005 PHE E 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 2040) covalent geometry : angle 0.56113 ( 2766) *********************** 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 62 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.069 Fit side-chains REVERT: E 61 GLU cc_start: 0.7748 (tp30) cc_final: 0.7514 (tt0) REVERT: F 61 GLU cc_start: 0.8010 (tp30) cc_final: 0.7403 (tt0) REVERT: C 83 GLU cc_start: 0.8523 (mp0) cc_final: 0.8169 (mp0) REVERT: D 58 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7595 (tttt) REVERT: D 61 GLU cc_start: 0.4550 (OUTLIER) cc_final: 0.3351 (pm20) outliers start: 19 outliers final: 18 residues processed: 53 average time/residue: 0.0261 time to fit residues: 1.9196 Evaluate side-chains 61 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.072 ------------------------------------------------------------------------------- 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 B residue 72 THR 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 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.5475 r_free = 0.5475 target = 0.356775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5418 r_free = 0.5418 target = 0.271333 restraints weight = 2560.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5421 r_free = 0.5421 target = 0.266714 restraints weight = 5444.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.264808 restraints weight = 6137.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5438 r_free = 0.5438 target = 0.263155 restraints weight = 5173.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5442 r_free = 0.5442 target = 0.263333 restraints weight = 4888.912| |-----------------------------------------------------------------------------| r_work (final): 0.5332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2040 Z= 0.103 Angle : 0.506 4.873 2766 Z= 0.291 Chirality : 0.049 0.148 366 Planarity : 0.002 0.017 354 Dihedral : 4.018 15.552 300 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 8.85 % Allowed : 17.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.00 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE F 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2040) covalent geometry : angle 0.50554 ( 2766) *********************** 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 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.078 Fit side-chains REVERT: B 92 THR cc_start: 0.8251 (m) cc_final: 0.7980 (p) REVERT: F 61 GLU cc_start: 0.7886 (tp30) cc_final: 0.7644 (tt0) REVERT: D 58 LYS cc_start: 0.7487 (mtpt) cc_final: 0.6706 (tttt) outliers start: 17 outliers final: 14 residues processed: 49 average time/residue: 0.0280 time to fit residues: 1.8810 Evaluate side-chains 52 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 = 0.5293 r_free = 0.5293 target = 0.330683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.253662 restraints weight = 2613.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.251959 restraints weight = 6603.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.247290 restraints weight = 6437.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.244045 restraints weight = 6797.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.243542 restraints weight = 6827.160| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2040 Z= 0.280 Angle : 0.749 5.503 2766 Z= 0.434 Chirality : 0.056 0.155 366 Planarity : 0.004 0.019 354 Dihedral : 5.569 20.827 300 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.27 % Favored : 69.73 % Rotamer: Outliers : 8.85 % Allowed : 20.31 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.010 PHE F 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 2040) covalent geometry : angle 0.74898 ( 2766) *********************** 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 57 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.072 Fit side-chains REVERT: F 61 GLU cc_start: 0.8041 (tp30) cc_final: 0.7530 (tt0) REVERT: D 58 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7503 (tttt) REVERT: D 61 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.3595 (pm20) outliers start: 17 outliers final: 15 residues processed: 50 average time/residue: 0.0255 time to fit residues: 1.7897 Evaluate side-chains 55 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.5162 r_free = 0.5162 target = 0.202242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.146306 restraints weight = 2278.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.143251 restraints weight = 1922.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.145173 restraints weight = 2189.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.144522 restraints weight = 1770.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.144854 restraints weight = 1500.606| |-----------------------------------------------------------------------------| r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2040 Z= 0.137 Angle : 0.611 5.426 2766 Z= 0.347 Chirality : 0.050 0.151 366 Planarity : 0.003 0.020 354 Dihedral : 4.412 16.655 300 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.99 % Favored : 84.01 % Rotamer: Outliers : 8.85 % Allowed : 19.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE E 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2040) covalent geometry : angle 0.61110 ( 2766) *********************** 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 60 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.084 Fit side-chains REVERT: F 61 GLU cc_start: 0.8140 (tp30) cc_final: 0.7652 (tt0) REVERT: D 58 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7639 (tttt) REVERT: D 61 GLU cc_start: 0.4478 (OUTLIER) cc_final: 0.3372 (pm20) outliers start: 17 outliers final: 14 residues processed: 51 average time/residue: 0.0274 time to fit residues: 1.9304 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 : 0.078 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 2.3394 ------------------------------------------------------------------------------- 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 = 0.5354 r_free = 0.5354 target = 0.339533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.246008 restraints weight = 2591.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.244544 restraints weight = 5121.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.243709 restraints weight = 5142.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.242177 restraints weight = 5101.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.241158 restraints weight = 5413.311| |-----------------------------------------------------------------------------| r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2040 Z= 0.173 Angle : 0.642 5.536 2766 Z= 0.366 Chirality : 0.051 0.154 366 Planarity : 0.003 0.020 354 Dihedral : 4.759 17.976 300 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.47 % Favored : 76.53 % Rotamer: Outliers : 8.33 % Allowed : 21.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.005 PHE A 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2040) covalent geometry : angle 0.64212 ( 2766) ********************** 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 60 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7303 (tttt) REVERT: D 61 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.3537 (pm20) outliers start: 16 outliers final: 15 residues processed: 52 average time/residue: 0.0236 time to fit residues: 1.7106 Evaluate side-chains 58 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.5362 r_free = 0.5362 target = 0.341376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.248411 restraints weight = 2618.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.242964 restraints weight = 4949.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.5290 r_free = 0.5290 target = 0.238888 restraints weight = 6068.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.238994 restraints weight = 5264.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.237490 restraints weight = 4882.101| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2040 Z= 0.166 Angle : 0.634 5.629 2766 Z= 0.361 Chirality : 0.051 0.155 366 Planarity : 0.003 0.020 354 Dihedral : 4.629 16.799 300 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.15 % Favored : 75.85 % Rotamer: Outliers : 8.85 % Allowed : 21.35 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.005 PHE E 94 HIS 0.004 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 2040) covalent geometry : angle 0.63397 ( 2766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 567.12 seconds wall clock time: 10 minutes 41.52 seconds (641.52 seconds total)