Starting phenix.real_space_refine on Mon Feb 10 19:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjq_4566/02_2025/6qjq_4566_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjq_4566/02_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_4566/02_2025/6qjq_4566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjq_4566/02_2025/6qjq_4566.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjq_4566/02_2025/6qjq_4566_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjq_4566/02_2025/6qjq_4566_neut.cif" } resolution = 3.7 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= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: "E" 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: D, F, C, B Time building chain proxies: 0.81, per 1000 atoms: 0.67 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: 0.25 Conformation dependent library (CDL) restraints added in 589.8 milliseconds 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: 0.19 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: 0.21 Time building geometry restraints manager: 0.30 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.830 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- 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= 1.432 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (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 HIS 0.005 0.002 HIS F 329 TYR 0.039 0.010 TYR A 310 *********************** 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 : 0.239 Fit side-chains REVERT: D 325 LEU cc_start: 0.8831 (mt) cc_final: 0.8510 (mp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0917 time to fit residues: 5.2563 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.085194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.077251 restraints weight = 4230.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.079246 restraints weight = 1866.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.080460 restraints weight = 1092.651| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1236 Z= 0.164 Angle : 0.688 8.127 1656 Z= 0.320 Chirality : 0.052 0.139 198 Planarity : 0.003 0.022 198 Dihedral : 4.118 18.472 162 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % 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 (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: -3.54 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 TYR 0.011 0.002 TYR A 310 *********************** 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: 3 poor density : 23 time to evaluate : 0.159 Fit side-chains REVERT: F 314 ASP cc_start: 0.8539 (t0) cc_final: 0.8276 (t0) REVERT: F 315 LEU cc_start: 0.9369 (mt) cc_final: 0.8998 (pt) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.0752 time to fit residues: 2.4632 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 313 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.077226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.070043 restraints weight = 4746.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.071661 restraints weight = 1995.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.072639 restraints weight = 1187.363| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1236 Z= 0.246 Angle : 0.661 8.094 1656 Z= 0.311 Chirality : 0.052 0.137 198 Planarity : 0.003 0.017 198 Dihedral : 4.350 17.025 162 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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: -3.35 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.012 0.002 TYR A 310 *********************** 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 25 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.171 Fit side-chains REVERT: F 314 ASP cc_start: 0.8617 (t0) cc_final: 0.8349 (t0) REVERT: F 315 LEU cc_start: 0.9404 (mt) cc_final: 0.8988 (pt) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0736 time to fit residues: 2.3540 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.075909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.068855 restraints weight = 4874.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.070410 restraints weight = 2034.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.071344 restraints weight = 1229.422| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 1236 Z= 0.342 Angle : 0.681 6.287 1656 Z= 0.327 Chirality : 0.053 0.127 198 Planarity : 0.004 0.024 198 Dihedral : 4.757 14.565 162 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.39 % Allowed : 15.28 % 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 (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: -3.30 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 329 TYR 0.013 0.003 TYR E 310 *********************** 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 22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.163 Fit side-chains REVERT: F 315 LEU cc_start: 0.9425 (mt) cc_final: 0.8991 (pt) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1090 time to fit residues: 2.8727 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain D residue 274 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4164 r_free = 0.4164 target = 0.103714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.093482 restraints weight = 4165.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.095383 restraints weight = 1683.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.096494 restraints weight = 909.595| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4932 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= 0.134 Angle : 0.626 6.970 1656 Z= 0.279 Chirality : 0.051 0.128 198 Planarity : 0.003 0.024 198 Dihedral : 4.028 12.816 162 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % 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: -3.17 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 TYR 0.014 0.002 TYR D 310 *********************** 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 25 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.163 Fit side-chains REVERT: F 314 ASP cc_start: 0.8472 (t0) cc_final: 0.8151 (t0) REVERT: F 315 LEU cc_start: 0.9325 (mt) cc_final: 0.8834 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0829 time to fit residues: 2.5930 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 : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 0.0370 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 overall best weight: 0.8618 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.082031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.074468 restraints weight = 4516.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.076188 restraints weight = 1885.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.077296 restraints weight = 1113.317| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5164 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= 0.132 Angle : 0.631 7.098 1656 Z= 0.282 Chirality : 0.050 0.125 198 Planarity : 0.003 0.023 198 Dihedral : 4.101 11.759 162 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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 (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: -3.16 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 TYR 0.011 0.001 TYR D 310 *********************** 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: 2 poor density : 20 time to evaluate : 0.166 Fit side-chains REVERT: F 314 ASP cc_start: 0.8525 (t0) cc_final: 0.8122 (t0) REVERT: F 315 LEU cc_start: 0.9442 (mt) cc_final: 0.8883 (pt) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.0854 time to fit residues: 2.3569 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.075714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.068646 restraints weight = 5054.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070134 restraints weight = 2111.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.071021 restraints weight = 1290.771| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1236 Z= 0.316 Angle : 0.639 6.506 1656 Z= 0.301 Chirality : 0.052 0.140 198 Planarity : 0.003 0.027 198 Dihedral : 4.483 12.225 162 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % 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 (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: -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 HIS 0.005 0.001 HIS C 329 TYR 0.012 0.002 TYR A 310 *********************** 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 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.165 Fit side-chains REVERT: F 314 ASP cc_start: 0.8670 (t0) cc_final: 0.8462 (t0) REVERT: F 315 LEU cc_start: 0.9497 (mt) cc_final: 0.9039 (pt) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0903 time to fit residues: 1.9644 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 : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.077534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.070341 restraints weight = 4895.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.071943 restraints weight = 2062.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.072868 restraints weight = 1241.043| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1236 Z= 0.207 Angle : 0.627 6.816 1656 Z= 0.283 Chirality : 0.052 0.121 198 Planarity : 0.003 0.026 198 Dihedral : 4.273 11.931 162 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 15.28 % 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 (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: -3.28 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.007 0.002 TYR D 310 *********************** 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 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.160 Fit side-chains REVERT: F 314 ASP cc_start: 0.8627 (t0) cc_final: 0.8243 (t0) REVERT: F 315 LEU cc_start: 0.9480 (mt) cc_final: 0.8953 (pt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0857 time to fit residues: 2.1733 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.077490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.070215 restraints weight = 4839.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.071823 restraints weight = 2061.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.072752 restraints weight = 1246.153| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5269 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= 0.199 Angle : 0.613 6.972 1656 Z= 0.278 Chirality : 0.051 0.119 198 Planarity : 0.003 0.025 198 Dihedral : 4.221 11.583 162 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % 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: -3.24 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.007 0.002 TYR D 310 *********************** 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 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.127 Fit side-chains REVERT: F 315 LEU cc_start: 0.9471 (mt) cc_final: 0.8917 (pt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0892 time to fit residues: 2.2459 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.101233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.090057 restraints weight = 4386.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.091928 restraints weight = 1667.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.093072 restraints weight = 924.127| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1236 Z= 0.187 Angle : 0.655 9.175 1656 Z= 0.286 Chirality : 0.051 0.120 198 Planarity : 0.003 0.025 198 Dihedral : 4.118 11.303 162 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % 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: -3.16 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.008 0.002 TYR D 310 ********************** 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 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.156 Fit side-chains REVERT: F 314 ASP cc_start: 0.8283 (t0) cc_final: 0.8078 (t0) REVERT: F 315 LEU cc_start: 0.9228 (mt) cc_final: 0.8788 (pt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0590 time to fit residues: 1.6858 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 : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.079433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.072883 restraints weight = 4810.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.074522 restraints weight = 1934.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.075532 restraints weight = 1118.273| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1236 Z= 0.274 Angle : 0.680 9.441 1656 Z= 0.308 Chirality : 0.051 0.119 198 Planarity : 0.003 0.027 198 Dihedral : 4.360 12.263 162 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 15.28 % 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 (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: -3.23 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 TYR 0.010 0.002 TYR A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 800.70 seconds wall clock time: 15 minutes 25.56 seconds (925.56 seconds total)