Starting phenix.real_space_refine on Mon Feb 10 21:14:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag3_15414/02_2025/8ag3_15414.cif" } resolution = 3.47 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1668 2.51 5 N 436 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2632 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "D" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Time building chain proxies: 2.54, per 1000 atoms: 0.97 Number of scatterers: 2632 At special positions: 0 Unit cell: (78.49, 64.295, 64.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 508 8.00 N 436 7.00 C 1668 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: 0.62 Conformation dependent library (CDL) restraints added in 295.5 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 16.1% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 4.125A pdb=" N ILE D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.238A pdb=" N THR C 72 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 155 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 149 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.619A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.897A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 127 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.831A pdb=" N CYS D 112 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 145 " --> pdb=" O CYS D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 150 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 852 1.35 - 1.46: 557 1.46 - 1.58: 1237 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 2676 Sorted by residual: bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.38e-01 bond pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.45e-02 4.76e+03 7.44e-01 bond pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 bond pdb=" CA LYS D 7 " pdb=" CB LYS D 7 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.68e-02 3.54e+03 4.56e-01 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3542 1.78 - 3.55: 58 3.55 - 5.33: 4 5.33 - 7.11: 5 7.11 - 8.88: 1 Bond angle restraints: 3610 Sorted by residual: angle pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET D 43 " pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta sigma weight residual 110.19 114.05 -3.86 1.62e+00 3.81e-01 5.66e+00 ... (remaining 3605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1299 13.04 - 26.08: 225 26.08 - 39.11: 81 39.11 - 52.15: 37 52.15 - 65.19: 12 Dihedral angle restraints: 1654 sinusoidal: 694 harmonic: 960 Sorted by residual: dihedral pdb=" CA ASP C 128 " pdb=" CB ASP C 128 " pdb=" CG ASP C 128 " pdb=" OD1 ASP C 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 83 " pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " pdb=" OD1 ASP C 83 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " pdb=" CD LYS D 77 " ideal model delta sinusoidal sigma weight residual 60.00 117.48 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 238 0.028 - 0.057: 103 0.057 - 0.085: 37 0.085 - 0.113: 28 0.113 - 0.141: 6 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 409 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 79 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 80 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 43 " -0.005 2.00e-02 2.50e+03 9.79e-03 9.58e-01 pdb=" C MET D 43 " 0.017 2.00e-02 2.50e+03 pdb=" O MET D 43 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 44 " -0.006 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 59 2.69 - 3.25: 2329 3.25 - 3.80: 3801 3.80 - 4.35: 5021 4.35 - 4.90: 8610 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" O ASP C 48 " pdb=" ND2 ASN C 52 " model vdw 2.143 3.120 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.232 3.040 nonbonded pdb=" O GLN D 10 " pdb=" OH TYR D 101 " model vdw 2.294 3.040 nonbonded pdb=" N GLU C 44 " pdb=" OE1 GLU C 44 " model vdw 2.344 3.120 nonbonded pdb=" NH1 ARG D 23 " pdb=" O TYR D 106 " model vdw 2.350 3.120 ... (remaining 19815 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 '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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.790 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.002 0.048 2676 Z= 0.167 Angle : 0.600 8.883 3610 Z= 0.322 Chirality : 0.044 0.141 412 Planarity : 0.007 0.133 458 Dihedral : 17.158 65.191 1030 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.74 % Favored : 65.26 % 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: -1.45 (0.47), residues: 318 helix: 2.05 (0.79), residues: 50 sheet: -0.29 (0.51), residues: 112 loop : -2.61 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE D 15 TYR 0.009 0.001 TYR D 4 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: D 106 TYR cc_start: 0.8501 (m-80) cc_final: 0.8225 (m-80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1712 time to fit residues: 20.5006 Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110599 restraints weight = 3585.024| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.59 r_work: 0.3194 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.197 Angle : 0.549 5.819 3610 Z= 0.295 Chirality : 0.044 0.141 412 Planarity : 0.006 0.102 458 Dihedral : 4.394 12.484 350 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.95 % Allowed : 28.90 % Favored : 69.16 % 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: -1.26 (0.48), residues: 318 helix: 2.05 (0.80), residues: 50 sheet: 0.01 (0.53), residues: 102 loop : -2.45 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.010 0.002 TYR D 101 ARG 0.001 0.000 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.301 Fit side-chains REVERT: C 71 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7795 (p) REVERT: C 75 PHE cc_start: 0.8261 (m-80) cc_final: 0.7662 (m-80) REVERT: C 119 TYR cc_start: 0.8605 (m-80) cc_final: 0.8379 (m-80) REVERT: D 106 TYR cc_start: 0.8576 (m-80) cc_final: 0.8320 (m-80) REVERT: D 156 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8033 (mm) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.1677 time to fit residues: 21.0103 Evaluate side-chains 110 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108867 restraints weight = 3628.325| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.61 r_work: 0.3131 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2676 Z= 0.344 Angle : 0.609 6.891 3610 Z= 0.330 Chirality : 0.046 0.156 412 Planarity : 0.006 0.089 458 Dihedral : 4.826 12.655 350 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.19 % Allowed : 25.32 % Favored : 69.48 % 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: -1.44 (0.47), residues: 318 helix: 1.61 (0.78), residues: 50 sheet: -0.04 (0.53), residues: 102 loop : -2.51 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.004 0.001 HIS C 120 PHE 0.017 0.001 PHE C 133 TYR 0.014 0.002 TYR D 101 ARG 0.004 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7504 (mp0) cc_final: 0.6283 (mp0) REVERT: C 65 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 75 PHE cc_start: 0.8116 (m-80) cc_final: 0.7524 (m-80) REVERT: D 156 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.1697 time to fit residues: 22.9326 Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.0470 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.135266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110713 restraints weight = 3612.966| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.58 r_work: 0.3172 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.184 Angle : 0.538 6.994 3610 Z= 0.290 Chirality : 0.044 0.152 412 Planarity : 0.005 0.084 458 Dihedral : 4.512 12.992 350 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.22 % Allowed : 27.60 % Favored : 68.18 % 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: -1.30 (0.47), residues: 318 helix: 1.94 (0.78), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.48 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.010 0.001 TYR C 119 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 75 PHE cc_start: 0.8213 (m-80) cc_final: 0.7605 (m-80) REVERT: C 140 LYS cc_start: 0.8309 (tttp) cc_final: 0.7886 (tttp) REVERT: D 70 ASP cc_start: 0.8144 (t70) cc_final: 0.7849 (t70) REVERT: D 119 TYR cc_start: 0.7849 (m-10) cc_final: 0.7425 (m-80) REVERT: D 156 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8128 (mm) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.1573 time to fit residues: 20.3766 Evaluate side-chains 115 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106565 restraints weight = 3716.700| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.58 r_work: 0.3151 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2676 Z= 0.268 Angle : 0.566 6.885 3610 Z= 0.306 Chirality : 0.045 0.145 412 Planarity : 0.005 0.081 458 Dihedral : 4.653 13.394 350 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.22 % Allowed : 27.27 % Favored : 68.51 % 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: -1.32 (0.47), residues: 318 helix: 1.88 (0.78), residues: 50 sheet: 0.02 (0.53), residues: 102 loop : -2.48 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.016 0.001 PHE C 133 TYR 0.017 0.002 TYR D 101 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7111 (tm-30) REVERT: C 75 PHE cc_start: 0.8226 (m-80) cc_final: 0.7655 (m-80) REVERT: C 140 LYS cc_start: 0.8299 (tttp) cc_final: 0.7779 (tttp) REVERT: D 156 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8112 (mm) outliers start: 13 outliers final: 9 residues processed: 113 average time/residue: 0.1772 time to fit residues: 23.0919 Evaluate side-chains 117 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 9 optimal weight: 0.2980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.134534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109837 restraints weight = 3615.662| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.61 r_work: 0.3155 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2676 Z= 0.266 Angle : 0.566 7.049 3610 Z= 0.305 Chirality : 0.045 0.166 412 Planarity : 0.005 0.081 458 Dihedral : 4.649 14.595 350 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.57 % Allowed : 27.92 % Favored : 68.51 % 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: -1.29 (0.47), residues: 318 helix: 1.95 (0.79), residues: 50 sheet: 0.03 (0.52), residues: 102 loop : -2.47 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.016 0.002 TYR D 101 ARG 0.006 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7528 (mp0) cc_final: 0.6586 (mp0) REVERT: C 43 MET cc_start: 0.4255 (tpp) cc_final: 0.3809 (tmm) REVERT: C 65 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6816 (tm-30) REVERT: C 75 PHE cc_start: 0.8123 (m-80) cc_final: 0.7478 (m-80) REVERT: C 140 LYS cc_start: 0.8200 (tttp) cc_final: 0.7650 (tttp) REVERT: D 156 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8126 (mm) outliers start: 11 outliers final: 10 residues processed: 113 average time/residue: 0.1684 time to fit residues: 21.9962 Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.132088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107731 restraints weight = 3829.063| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.57 r_work: 0.3159 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2676 Z= 0.317 Angle : 0.594 5.729 3610 Z= 0.323 Chirality : 0.046 0.169 412 Planarity : 0.006 0.080 458 Dihedral : 4.826 15.223 350 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.87 % Allowed : 26.30 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.41 (0.46), residues: 318 helix: 1.75 (0.78), residues: 50 sheet: -0.03 (0.52), residues: 102 loop : -2.52 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.017 0.002 PHE C 133 TYR 0.012 0.002 TYR D 101 ARG 0.013 0.001 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.4467 (tpp) cc_final: 0.4013 (tmm) REVERT: C 60 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7937 (ttm-80) REVERT: C 65 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7125 (tm-30) REVERT: C 75 PHE cc_start: 0.8266 (m-80) cc_final: 0.7709 (m-80) REVERT: C 140 LYS cc_start: 0.8379 (tttp) cc_final: 0.7894 (tttp) REVERT: D 156 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8185 (mm) outliers start: 15 outliers final: 13 residues processed: 113 average time/residue: 0.1766 time to fit residues: 22.9340 Evaluate side-chains 122 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.132234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107641 restraints weight = 3678.389| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.64 r_work: 0.3137 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2676 Z= 0.304 Angle : 0.594 5.068 3610 Z= 0.322 Chirality : 0.046 0.163 412 Planarity : 0.006 0.081 458 Dihedral : 4.817 14.859 350 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.90 % Allowed : 27.27 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.47), residues: 318 helix: 1.68 (0.79), residues: 50 sheet: -0.06 (0.53), residues: 102 loop : -2.52 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.016 0.001 PHE C 133 TYR 0.015 0.002 TYR D 101 ARG 0.010 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4339 (tpp) cc_final: 0.3955 (tmm) REVERT: C 60 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7738 (ttm-80) REVERT: C 65 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6828 (tm-30) REVERT: C 75 PHE cc_start: 0.8119 (m-80) cc_final: 0.7525 (m-80) REVERT: C 140 LYS cc_start: 0.8195 (tttp) cc_final: 0.7655 (tttp) REVERT: D 156 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8091 (mm) outliers start: 12 outliers final: 11 residues processed: 112 average time/residue: 0.1690 time to fit residues: 22.0221 Evaluate side-chains 120 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.130460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106712 restraints weight = 3714.530| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.51 r_work: 0.3177 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2676 Z= 0.235 Angle : 0.559 5.152 3610 Z= 0.304 Chirality : 0.044 0.154 412 Planarity : 0.005 0.079 458 Dihedral : 4.676 14.682 350 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.22 % Allowed : 26.95 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.47), residues: 318 helix: 1.87 (0.80), residues: 50 sheet: -0.06 (0.53), residues: 102 loop : -2.49 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.015 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.010 0.001 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 MET cc_start: 0.4374 (tpp) cc_final: 0.3929 (tmm) REVERT: C 60 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7909 (ttm-80) REVERT: C 65 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 75 PHE cc_start: 0.8215 (m-80) cc_final: 0.7586 (m-80) REVERT: C 140 LYS cc_start: 0.8300 (tttp) cc_final: 0.7753 (tttp) REVERT: D 19 PHE cc_start: 0.8462 (m-80) cc_final: 0.8208 (m-80) REVERT: D 156 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.1713 time to fit residues: 22.0047 Evaluate side-chains 119 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 overall best weight: 0.2644 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108040 restraints weight = 3694.793| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.61 r_work: 0.3188 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2676 Z= 0.156 Angle : 0.528 5.255 3610 Z= 0.285 Chirality : 0.044 0.148 412 Planarity : 0.005 0.079 458 Dihedral : 4.407 14.368 350 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.90 % Allowed : 27.92 % Favored : 68.18 % 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: -1.26 (0.47), residues: 318 helix: 2.14 (0.83), residues: 50 sheet: -0.05 (0.53), residues: 102 loop : -2.43 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.009 0.001 TYR D 101 ARG 0.009 0.000 ARG C 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7543 (mp0) cc_final: 0.6748 (mp0) REVERT: C 43 MET cc_start: 0.4355 (tpp) cc_final: 0.3934 (tmm) REVERT: C 65 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 71 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7775 (p) REVERT: C 75 PHE cc_start: 0.8111 (m-80) cc_final: 0.7435 (m-80) REVERT: C 140 LYS cc_start: 0.8199 (tttp) cc_final: 0.7637 (tttp) REVERT: D 19 PHE cc_start: 0.8412 (m-80) cc_final: 0.8168 (m-80) REVERT: D 70 ASP cc_start: 0.7991 (t70) cc_final: 0.7739 (t70) REVERT: D 106 TYR cc_start: 0.8578 (m-80) cc_final: 0.8322 (m-80) REVERT: D 119 TYR cc_start: 0.7673 (m-10) cc_final: 0.7347 (m-80) REVERT: D 129 LYS cc_start: 0.8256 (mmtm) cc_final: 0.8036 (mttp) REVERT: D 156 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8063 (mm) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.1600 time to fit residues: 20.0295 Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106470 restraints weight = 3722.260| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.53 r_work: 0.3173 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2676 Z= 0.261 Angle : 0.584 7.123 3610 Z= 0.312 Chirality : 0.046 0.200 412 Planarity : 0.005 0.079 458 Dihedral : 4.633 16.097 350 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.25 % Allowed : 27.27 % Favored : 69.48 % 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: -1.30 (0.47), residues: 318 helix: 1.94 (0.80), residues: 50 sheet: -0.02 (0.53), residues: 102 loop : -2.44 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.012 0.002 TYR D 101 ARG 0.008 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.56 seconds wall clock time: 33 minutes 19.43 seconds (1999.43 seconds total)