Starting phenix.real_space_refine on Fri Aug 22 12:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjq_4566/08_2025/6qjq_4566_neut.cif" } resolution = 3.7 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= 0.003 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 6 5.16 5 C 774 2.51 5 N 222 2.21 5 O 216 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1218 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 207 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Restraints were copied for chains: B, C, E, F Time building chain proxies: 0.22, per 1000 atoms: 0.18 Number of scatterers: 1218 At special positions: 0 Unit cell: (95.68, 61.36, 39.52, 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 6 16.00 O 216 8.00 N 222 7.00 C 774 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: 0.15 Conformation dependent library (CDL) restraints added in 29.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.000A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.144A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.422A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 328 removed outlier: 7.276A pdb=" N ILE B 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.521A pdb=" N VAL D 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL E 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.912A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 321 through 329 removed outlier: 7.188A pdb=" N CYS D 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU E 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN E 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY D 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N HIS E 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N CYS D 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N LEU F 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N SER D 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASN F 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY D 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 15 hydrogen bonds defined for protein. 45 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: 0.07 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 336 1.34 - 1.46: 145 1.46 - 1.57: 695 1.57 - 1.69: 54 1.69 - 1.80: 6 Bond restraints: 1236 Sorted by residual: bond pdb=" CA LYS B 311 " pdb=" C LYS B 311 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.04e-02 9.25e+03 3.02e+01 bond pdb=" CA LYS A 311 " pdb=" C LYS A 311 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.04e-02 9.25e+03 3.02e+01 bond pdb=" CA LYS C 311 " pdb=" C LYS C 311 " ideal model delta sigma weight residual 1.525 1.581 -0.057 1.04e-02 9.25e+03 2.98e+01 bond pdb=" CA ILE F 328 " pdb=" CB ILE F 328 " ideal model delta sigma weight residual 1.537 1.598 -0.061 1.17e-02 7.31e+03 2.70e+01 bond pdb=" CA ILE D 328 " pdb=" CB ILE D 328 " ideal model delta sigma weight residual 1.537 1.598 -0.061 1.17e-02 7.31e+03 2.68e+01 ... (remaining 1231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 1344 1.21 - 2.41: 217 2.41 - 3.62: 62 3.62 - 4.83: 24 4.83 - 6.03: 9 Bond angle restraints: 1656 Sorted by residual: angle pdb=" N LYS C 317 " pdb=" CA LYS C 317 " pdb=" C LYS C 317 " ideal model delta sigma weight residual 108.02 114.05 -6.03 1.75e+00 3.27e-01 1.19e+01 angle pdb=" N LYS A 317 " pdb=" CA LYS A 317 " pdb=" C LYS A 317 " ideal model delta sigma weight residual 108.02 114.05 -6.03 1.75e+00 3.27e-01 1.19e+01 angle pdb=" N LYS B 317 " pdb=" CA LYS B 317 " pdb=" C LYS B 317 " ideal model delta sigma weight residual 108.02 114.03 -6.01 1.75e+00 3.27e-01 1.18e+01 angle pdb=" N LYS D 311 " pdb=" CA LYS D 311 " pdb=" C LYS D 311 " ideal model delta sigma weight residual 108.21 113.85 -5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" N LYS F 311 " pdb=" CA LYS F 311 " pdb=" C LYS F 311 " ideal model delta sigma weight residual 108.21 113.84 -5.63 2.00e+00 2.50e-01 7.91e+00 ... (remaining 1651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.33: 648 10.33 - 20.66: 42 20.66 - 30.98: 33 30.98 - 41.31: 9 41.31 - 51.64: 12 Dihedral angle restraints: 744 sinusoidal: 294 harmonic: 450 Sorted by residual: dihedral pdb=" C LYS D 311 " pdb=" N LYS D 311 " pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta harmonic sigma weight residual -122.60 -130.30 7.70 0 2.50e+00 1.60e-01 9.48e+00 dihedral pdb=" C LYS F 311 " pdb=" N LYS F 311 " pdb=" CA LYS F 311 " pdb=" CB LYS F 311 " ideal model delta harmonic sigma weight residual -122.60 -130.24 7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" C LYS E 311 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " pdb=" CB LYS E 311 " ideal model delta harmonic sigma weight residual -122.60 -130.22 7.62 0 2.50e+00 1.60e-01 9.28e+00 ... (remaining 741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 74 0.048 - 0.096: 41 0.096 - 0.145: 43 0.145 - 0.193: 20 0.193 - 0.241: 20 Chirality restraints: 198 Sorted by residual: chirality pdb=" CA ILE F 328 " pdb=" N ILE F 328 " pdb=" C ILE F 328 " pdb=" CB ILE F 328 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL C 318 " pdb=" N VAL C 318 " pdb=" C VAL C 318 " pdb=" CB VAL C 318 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 195 not shown) Planarity restraints: 198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR A 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.07e+00 pdb=" CG TYR B 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.03e+00 pdb=" CG TYR C 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.004 2.00e-02 2.50e+03 ... (remaining 195 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 445 2.98 - 3.46: 935 3.46 - 3.94: 1837 3.94 - 4.42: 1701 4.42 - 4.90: 3218 Nonbonded interactions: 8136 Sorted by model distance: nonbonded pdb=" OD1 ASN A 327 " pdb=" ND2 ASN C 327 " model vdw 2.499 3.120 nonbonded pdb=" O SER A 324 " pdb=" N LEU C 325 " model vdw 2.526 3.120 nonbonded pdb=" N LEU D 315 " pdb=" O ASP F 314 " model vdw 2.529 3.120 nonbonded pdb=" O GLY A 326 " pdb=" N ASN C 327 " model vdw 2.566 3.120 nonbonded pdb=" O PRO A 312 " pdb=" N VAL C 313 " model vdw 2.578 3.120 ... (remaining 8131 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.090 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.021 0.061 1236 Z= 1.465 Angle : 1.173 6.033 1656 Z= 0.669 Chirality : 0.112 0.241 198 Planarity : 0.009 0.031 198 Dihedral : 13.356 51.641 456 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 2.00 % Allowed : 4.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.41 (0.49), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.38), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.039 0.010 TYR A 310 HIS 0.005 0.002 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.02084 ( 1236) covalent geometry : angle 1.17347 ( 1656) hydrogen bonds : bond 0.27093 ( 15) hydrogen bonds : angle 10.28239 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.029 Fit side-chains REVERT: D 325 LEU cc_start: 0.8831 (mt) cc_final: 0.8509 (mp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0196 time to fit residues: 1.1233 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.081736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.074098 restraints weight = 4452.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.075925 restraints weight = 1933.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.077029 restraints weight = 1140.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.077674 restraints weight = 795.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.078171 restraints weight = 608.313| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1236 Z= 0.135 Angle : 0.699 7.840 1656 Z= 0.336 Chirality : 0.053 0.142 198 Planarity : 0.004 0.021 198 Dihedral : 4.292 18.724 162 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.17 % Allowed : 9.03 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 310 HIS 0.002 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 1236) covalent geometry : angle 0.69876 ( 1656) hydrogen bonds : bond 0.03087 ( 15) hydrogen bonds : angle 5.88819 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.030 Fit side-chains REVERT: F 314 ASP cc_start: 0.8552 (t0) cc_final: 0.8311 (t0) REVERT: F 315 LEU cc_start: 0.9323 (mt) cc_final: 0.8958 (pt) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.0176 time to fit residues: 0.5783 Evaluate side-chains 22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 328 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.076754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.069489 restraints weight = 4790.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.071121 restraints weight = 1990.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.072125 restraints weight = 1178.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.072762 restraints weight = 835.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.073164 restraints weight = 655.829| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1236 Z= 0.182 Angle : 0.662 6.319 1656 Z= 0.317 Chirality : 0.053 0.143 198 Planarity : 0.003 0.016 198 Dihedral : 4.407 17.181 162 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.47 % Allowed : 12.50 % Favored : 84.03 % 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 aren not related in a simple way. whole: -3.35 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR A 310 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 1236) covalent geometry : angle 0.66157 ( 1656) hydrogen bonds : bond 0.02943 ( 15) hydrogen bonds : angle 5.54950 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.030 Fit side-chains REVERT: F 314 ASP cc_start: 0.8627 (t0) cc_final: 0.8371 (t0) REVERT: F 315 LEU cc_start: 0.9374 (mt) cc_final: 0.9016 (pt) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.0191 time to fit residues: 0.5779 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 328 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.0010 chunk 11 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.105871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.095322 restraints weight = 4231.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.097464 restraints weight = 1655.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.098622 restraints weight = 868.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.099390 restraints weight = 542.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.099786 restraints weight = 371.948| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1236 Z= 0.079 Angle : 0.614 7.142 1656 Z= 0.274 Chirality : 0.050 0.136 198 Planarity : 0.003 0.016 198 Dihedral : 3.870 13.479 162 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.69 % Allowed : 14.58 % Favored : 84.72 % 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 aren not related in a simple way. whole: -3.24 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR D 310 HIS 0.003 0.000 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00167 ( 1236) covalent geometry : angle 0.61425 ( 1656) hydrogen bonds : bond 0.02507 ( 15) hydrogen bonds : angle 4.64074 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.035 Fit side-chains REVERT: F 314 ASP cc_start: 0.8317 (t0) cc_final: 0.7982 (t0) REVERT: F 315 LEU cc_start: 0.9251 (mt) cc_final: 0.8790 (pt) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.0246 time to fit residues: 0.6993 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 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 = 0.3967 r_free = 0.3967 target = 0.076452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.069133 restraints weight = 4843.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.070686 restraints weight = 2055.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.071691 restraints weight = 1244.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.072299 restraints weight = 898.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.072665 restraints weight = 718.640| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1236 Z= 0.191 Angle : 0.671 8.126 1656 Z= 0.316 Chirality : 0.052 0.137 198 Planarity : 0.003 0.024 198 Dihedral : 4.560 12.858 162 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.78 % Allowed : 14.58 % Favored : 82.64 % 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 aren not related in a simple way. whole: -3.28 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR A 310 HIS 0.004 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 1236) covalent geometry : angle 0.67057 ( 1656) hydrogen bonds : bond 0.02609 ( 15) hydrogen bonds : angle 4.92807 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.057 Fit side-chains REVERT: F 315 LEU cc_start: 0.9412 (mt) cc_final: 0.8933 (pt) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0327 time to fit residues: 0.9598 Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.072152 restraints weight = 4763.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.073904 restraints weight = 1971.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.074940 restraints weight = 1163.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.075655 restraints weight = 834.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.076122 restraints weight = 648.364| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1236 Z= 0.100 Angle : 0.619 7.741 1656 Z= 0.282 Chirality : 0.051 0.147 198 Planarity : 0.003 0.023 198 Dihedral : 4.173 12.288 162 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.69 % Allowed : 15.97 % Favored : 83.33 % 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 aren not related in a simple way. whole: -3.21 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR D 310 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 1236) covalent geometry : angle 0.61921 ( 1656) hydrogen bonds : bond 0.02249 ( 15) hydrogen bonds : angle 4.51688 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.052 Fit side-chains REVERT: F 314 ASP cc_start: 0.8510 (t0) cc_final: 0.8131 (t0) REVERT: F 315 LEU cc_start: 0.9391 (mt) cc_final: 0.8891 (pt) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.0304 time to fit residues: 0.8413 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 2.5902 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.078167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070700 restraints weight = 4686.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.072347 restraints weight = 2004.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.073343 restraints weight = 1211.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.073875 restraints weight = 869.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.074378 restraints weight = 706.478| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1236 Z= 0.136 Angle : 0.669 9.351 1656 Z= 0.301 Chirality : 0.051 0.153 198 Planarity : 0.003 0.024 198 Dihedral : 4.178 11.395 162 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.69 % Allowed : 17.36 % Favored : 81.94 % 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 aren not related in a simple way. whole: -3.25 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 310 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 1236) covalent geometry : angle 0.66854 ( 1656) hydrogen bonds : bond 0.02252 ( 15) hydrogen bonds : angle 4.61234 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.056 Fit side-chains REVERT: F 310 TYR cc_start: 0.8828 (t80) cc_final: 0.8579 (t80) REVERT: F 314 ASP cc_start: 0.8540 (t0) cc_final: 0.8330 (t0) REVERT: F 315 LEU cc_start: 0.9431 (mt) cc_final: 0.8895 (pt) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0358 time to fit residues: 0.8563 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 327 ASN ** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.075784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.068659 restraints weight = 5061.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.070202 restraints weight = 2116.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.071125 restraints weight = 1281.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.071641 restraints weight = 928.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.072041 restraints weight = 749.711| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1236 Z= 0.191 Angle : 0.687 9.604 1656 Z= 0.318 Chirality : 0.052 0.155 198 Planarity : 0.004 0.026 198 Dihedral : 4.429 12.325 162 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.39 % Allowed : 16.67 % Favored : 81.94 % 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 aren not related in a simple way. whole: -3.32 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 310 HIS 0.004 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 1236) covalent geometry : angle 0.68654 ( 1656) hydrogen bonds : bond 0.02464 ( 15) hydrogen bonds : angle 4.96016 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.055 Fit side-chains REVERT: F 315 LEU cc_start: 0.9438 (mt) cc_final: 0.8988 (pt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0223 time to fit residues: 0.5540 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.079119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.071680 restraints weight = 4605.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.073283 restraints weight = 1948.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.074292 restraints weight = 1177.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.074899 restraints weight = 846.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.075351 restraints weight = 672.885| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1236 Z= 0.107 Angle : 0.632 9.342 1656 Z= 0.289 Chirality : 0.051 0.141 198 Planarity : 0.003 0.025 198 Dihedral : 4.118 11.370 162 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % 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 aren not related in a simple way. whole: -3.26 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR D 310 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 1236) covalent geometry : angle 0.63243 ( 1656) hydrogen bonds : bond 0.02245 ( 15) hydrogen bonds : angle 4.39922 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.052 Fit side-chains REVERT: F 314 ASP cc_start: 0.8381 (t0) cc_final: 0.8019 (t0) REVERT: F 315 LEU cc_start: 0.9430 (mt) cc_final: 0.8886 (pt) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0219 time to fit residues: 0.6377 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 329 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 = 0.3985 r_free = 0.3985 target = 0.077231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.069830 restraints weight = 4874.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.071430 restraints weight = 2057.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.072437 restraints weight = 1247.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.072990 restraints weight = 901.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.073139 restraints weight = 729.892| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1236 Z= 0.142 Angle : 0.669 8.957 1656 Z= 0.303 Chirality : 0.052 0.151 198 Planarity : 0.003 0.025 198 Dihedral : 4.193 12.031 162 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.69 % Allowed : 18.75 % Favored : 80.56 % 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 aren not related in a simple way. whole: -3.34 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 310 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 1236) covalent geometry : angle 0.66863 ( 1656) hydrogen bonds : bond 0.02206 ( 15) hydrogen bonds : angle 4.57704 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.064 Fit side-chains REVERT: F 314 ASP cc_start: 0.8465 (t0) cc_final: 0.8097 (t0) REVERT: F 315 LEU cc_start: 0.9457 (mt) cc_final: 0.8971 (pt) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0195 time to fit residues: 0.5276 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 329 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 = 0.4109 r_free = 0.4109 target = 0.098368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.087023 restraints weight = 4515.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.088916 restraints weight = 1770.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.089983 restraints weight = 983.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.090708 restraints weight = 649.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.091203 restraints weight = 465.903| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1236 Z= 0.189 Angle : 0.666 9.282 1656 Z= 0.313 Chirality : 0.052 0.153 198 Planarity : 0.004 0.027 198 Dihedral : 4.337 12.099 162 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.69 % Allowed : 18.75 % Favored : 80.56 % 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 aren not related in a simple way. whole: -3.35 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 310 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 1236) covalent geometry : angle 0.66637 ( 1656) hydrogen bonds : bond 0.02427 ( 15) hydrogen bonds : angle 4.87553 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 425.22 seconds wall clock time: 8 minutes 17.73 seconds (497.73 seconds total)