Starting phenix.real_space_refine on Sat Apr 26 14:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qjq_4566/04_2025/6qjq_4566_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qjq_4566/04_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_4566/04_2025/6qjq_4566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qjq_4566/04_2025/6qjq_4566.map" model { file = "/net/cci-nas-00/data/ceres_data/6qjq_4566/04_2025/6qjq_4566_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qjq_4566/04_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-5669/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: 0.80, per 1000 atoms: 0.66 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: 0.22 Conformation dependent library (CDL) restraints added in 463.7 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: 0.16 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: 0.20 Time building geometry restraints manager: 0.27 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: 0.780 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: 0.010 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.27093 ( 15) hydrogen bonds : angle 10.28239 ( 45) covalent geometry : bond 0.02084 ( 1236) covalent geometry : angle 1.17347 ( 1656) *********************** 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 : 0.166 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: 0.0888 time to fit residues: 5.0084 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 : 0.153 ------------------------------------------------------------------------------- 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: 5.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.085958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.077960 restraints weight = 4176.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.079955 restraints weight = 1850.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.081161 restraints weight = 1084.883| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1236 Z= 0.110 Angle : 0.682 8.171 1656 Z= 0.317 Chirality : 0.052 0.137 198 Planarity : 0.003 0.021 198 Dihedral : 4.089 18.724 162 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.78 % Allowed : 9.72 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 TYR 0.010 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 15) hydrogen bonds : angle 5.59259 ( 45) covalent geometry : bond 0.00235 ( 1236) covalent geometry : angle 0.68232 ( 1656) *********************** 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 28 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.139 Fit side-chains REVERT: F 314 ASP cc_start: 0.8511 (t0) cc_final: 0.8250 (t0) REVERT: F 315 LEU cc_start: 0.9348 (mt) cc_final: 0.8979 (pt) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0701 time to fit residues: 2.4003 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 : 0.166 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.0010 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.078075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.070692 restraints weight = 4660.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.072342 restraints weight = 1997.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.073328 restraints weight = 1193.055| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4258 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= 0.139 Angle : 0.646 8.020 1656 Z= 0.300 Chirality : 0.051 0.136 198 Planarity : 0.003 0.018 198 Dihedral : 4.141 16.700 162 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.69 % Allowed : 13.89 % 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: -3.36 (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 0.000 HIS C 329 TYR 0.011 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 15) hydrogen bonds : angle 5.25825 ( 45) covalent geometry : bond 0.00326 ( 1236) covalent geometry : angle 0.64601 ( 1656) *********************** 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: 1 poor density : 23 time to evaluate : 0.152 Fit side-chains REVERT: C 328 ILE cc_start: 0.8498 (mt) cc_final: 0.8138 (mt) REVERT: F 314 ASP cc_start: 0.8581 (t0) cc_final: 0.8294 (t0) REVERT: F 315 LEU cc_start: 0.9399 (mt) cc_final: 0.8930 (pt) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.0762 time to fit residues: 2.3039 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.077179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.069817 restraints weight = 4681.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.071540 restraints weight = 1983.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.072466 restraints weight = 1175.738| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1236 Z= 0.184 Angle : 0.643 6.503 1656 Z= 0.308 Chirality : 0.053 0.141 198 Planarity : 0.003 0.019 198 Dihedral : 4.512 14.797 162 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.08 % Allowed : 15.28 % 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 (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: -3.25 (0.51), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.39), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 TYR 0.011 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 15) hydrogen bonds : angle 4.99258 ( 45) covalent geometry : bond 0.00422 ( 1236) covalent geometry : angle 0.64266 ( 1656) *********************** 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 24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.159 Fit side-chains REVERT: F 315 LEU cc_start: 0.9448 (mt) cc_final: 0.8964 (pt) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0779 time to fit residues: 2.2407 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain F residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.082159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.074496 restraints weight = 4224.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.076326 restraints weight = 1792.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.077463 restraints weight = 1059.802| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1236 Z= 0.084 Angle : 0.645 9.030 1656 Z= 0.283 Chirality : 0.051 0.134 198 Planarity : 0.003 0.020 198 Dihedral : 3.925 12.103 162 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 : 0.69 % 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 (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: -3.09 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 329 TYR 0.013 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.02348 ( 15) hydrogen bonds : angle 4.48276 ( 45) covalent geometry : bond 0.00182 ( 1236) covalent geometry : angle 0.64457 ( 1656) *********************** 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: 1 poor density : 24 time to evaluate : 0.158 Fit side-chains REVERT: F 314 ASP cc_start: 0.8557 (t0) cc_final: 0.8156 (t0) REVERT: F 315 LEU cc_start: 0.9372 (mt) cc_final: 0.8876 (pt) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0782 time to fit residues: 2.4580 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 SER 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: 7.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.079303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.071954 restraints weight = 4705.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.073658 restraints weight = 1979.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.074671 restraints weight = 1178.986| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5069 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= 0.131 Angle : 0.618 6.729 1656 Z= 0.289 Chirality : 0.051 0.134 198 Planarity : 0.003 0.023 198 Dihedral : 4.331 11.270 162 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % 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 (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: -3.09 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 TYR 0.013 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.02307 ( 15) hydrogen bonds : angle 4.44801 ( 45) covalent geometry : bond 0.00312 ( 1236) covalent geometry : angle 0.61764 ( 1656) *********************** 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 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.154 Fit side-chains REVERT: F 315 LEU cc_start: 0.9430 (mt) cc_final: 0.8899 (pt) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0817 time to fit residues: 2.0693 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 : 0.155 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.076569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.069818 restraints weight = 5064.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.071316 restraints weight = 2150.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.072223 restraints weight = 1296.388| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 1236 Z= 0.252 Angle : 0.676 7.926 1656 Z= 0.327 Chirality : 0.054 0.142 198 Planarity : 0.004 0.028 198 Dihedral : 4.774 12.391 162 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % 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: -3.27 (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 HIS 0.005 0.001 HIS C 329 TYR 0.011 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 15) hydrogen bonds : angle 5.02685 ( 45) covalent geometry : bond 0.00579 ( 1236) covalent geometry : angle 0.67558 ( 1656) *********************** 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: 2 poor density : 16 time to evaluate : 0.160 Fit side-chains REVERT: F 315 LEU cc_start: 0.9461 (mt) cc_final: 0.9056 (pt) outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0603 time to fit residues: 1.5269 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain D 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: 7.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 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 = 0.3954 r_free = 0.3954 target = 0.076158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.069060 restraints weight = 4991.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.070613 restraints weight = 2108.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.071538 restraints weight = 1268.074| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1236 Z= 0.195 Angle : 0.642 6.573 1656 Z= 0.307 Chirality : 0.053 0.138 198 Planarity : 0.004 0.028 198 Dihedral : 4.628 12.779 162 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % 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 (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: -3.41 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 TYR 0.010 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.02699 ( 15) hydrogen bonds : angle 4.91854 ( 45) covalent geometry : bond 0.00440 ( 1236) covalent geometry : angle 0.64193 ( 1656) *********************** 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: 1 poor density : 16 time to evaluate : 0.156 Fit side-chains REVERT: F 315 LEU cc_start: 0.9448 (mt) cc_final: 0.8972 (pt) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0600 time to fit residues: 1.4298 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.077594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.070410 restraints weight = 4859.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.071987 restraints weight = 2064.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.072953 restraints weight = 1238.643| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5440 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= 0.146 Angle : 0.629 6.835 1656 Z= 0.293 Chirality : 0.052 0.136 198 Planarity : 0.003 0.026 198 Dihedral : 4.383 12.518 162 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.78 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 (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: -3.42 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.013 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 15) hydrogen bonds : angle 4.64829 ( 45) covalent geometry : bond 0.00329 ( 1236) covalent geometry : angle 0.62868 ( 1656) *********************** 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 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.145 Fit side-chains REVERT: F 314 ASP cc_start: 0.8649 (t0) cc_final: 0.8229 (t0) REVERT: F 315 LEU cc_start: 0.9473 (mt) cc_final: 0.9007 (pt) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0565 time to fit residues: 1.4858 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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: 9.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.097214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.085791 restraints weight = 4505.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.087643 restraints weight = 1764.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.088758 restraints weight = 967.235| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 1236 Z= 0.253 Angle : 0.674 6.513 1656 Z= 0.331 Chirality : 0.054 0.138 198 Planarity : 0.004 0.028 198 Dihedral : 4.805 12.768 162 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.39 % Allowed : 14.58 % 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 (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: -3.58 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.40), 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 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 15) hydrogen bonds : angle 5.29643 ( 45) covalent geometry : bond 0.00575 ( 1236) covalent geometry : angle 0.67429 ( 1656) ********************** 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: 2 poor density : 17 time to evaluate : 0.177 Fit side-chains REVERT: F 315 LEU cc_start: 0.9351 (mt) cc_final: 0.8954 (pt) outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0620 time to fit residues: 1.6858 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain D residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 0.1980 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.100059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.088793 restraints weight = 4480.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.090735 restraints weight = 1765.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.091869 restraints weight = 965.339| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5591 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= 0.122 Angle : 0.630 7.160 1656 Z= 0.295 Chirality : 0.052 0.136 198 Planarity : 0.004 0.028 198 Dihedral : 4.326 12.459 162 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.39 % Allowed : 14.58 % 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 (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: -3.49 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 TYR 0.015 0.002 TYR D 310 Details of bonding type rmsd hydrogen bonds : bond 0.02456 ( 15) hydrogen bonds : angle 4.62242 ( 45) covalent geometry : bond 0.00273 ( 1236) covalent geometry : angle 0.63034 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 846.12 seconds wall clock time: 15 minutes 23.07 seconds (923.07 seconds total)