Starting phenix.real_space_refine on Wed Jun 4 09:43:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcp_37445/06_2025/8wcp_37445.cif" } resolution = 3.28 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= 0.000 sd= 0.001 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 954 2.51 5 N 285 2.21 5 O 291 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-5710/modules/chem_data/mon_lib" Total number of atoms: 1536 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: C, B, D, F, I, H Time building chain proxies: 1.11, per 1000 atoms: 0.72 Number of scatterers: 1536 At special positions: 0 Unit cell: (91.3, 87.15, 34.03, 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 291 8.00 N 285 7.00 C 954 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: 1.03 Conformation dependent library (CDL) restraints added in 161.6 milliseconds 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 414 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 46.4% 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 275 through 280 removed outlier: 6.370A pdb=" N GLN A 276 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 278 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 284 through 288 removed outlier: 5.916A pdb=" N SER A 285 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN B 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 287 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 297 through 302 removed outlier: 5.612A pdb=" N LYS A 298 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 301 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 300 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS C 298 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.665A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 323 removed outlier: 6.154A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N GLY B 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.318A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 75 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: 0.26 Time building geometry restraints manager: 1.11 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: 513 1.34 - 1.46: 146 1.46 - 1.57: 874 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 1539 Sorted by residual: bond pdb=" CA THR B 319 " pdb=" C THR B 319 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 7.64e-01 bond pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 7.45e-01 bond pdb=" CA UNK F 336 " pdb=" CB UNK F 336 " ideal model delta sigma weight residual 1.530 1.513 0.017 2.00e-02 2.50e+03 7.34e-01 bond pdb=" CA THR C 319 " pdb=" C THR C 319 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 7.24e-01 bond pdb=" CA UNK E 336 " pdb=" CB UNK E 336 " ideal model delta sigma weight residual 1.530 1.513 0.017 2.00e-02 2.50e+03 7.15e-01 ... (remaining 1534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 1965 1.57 - 3.14: 72 3.14 - 4.72: 21 4.72 - 6.29: 3 6.29 - 7.86: 3 Bond angle restraints: 2064 Sorted by residual: angle pdb=" N LEU B 284 " pdb=" CA LEU B 284 " pdb=" C LEU B 284 " ideal model delta sigma weight residual 107.37 99.51 7.86 2.07e+00 2.33e-01 1.44e+01 angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 107.37 99.54 7.83 2.07e+00 2.33e-01 1.43e+01 angle pdb=" N LEU A 284 " pdb=" CA LEU A 284 " pdb=" C LEU A 284 " ideal model delta sigma weight residual 107.37 99.54 7.83 2.07e+00 2.33e-01 1.43e+01 angle pdb=" N THR C 319 " pdb=" CA THR C 319 " pdb=" C THR C 319 " ideal model delta sigma weight residual 110.14 115.01 -4.87 1.55e+00 4.16e-01 9.86e+00 angle pdb=" N THR A 319 " pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 110.14 115.00 -4.86 1.55e+00 4.16e-01 9.85e+00 ... (remaining 2059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.26: 773 8.26 - 16.52: 115 16.52 - 24.78: 33 24.78 - 33.04: 18 33.04 - 41.31: 9 Dihedral angle restraints: 948 sinusoidal: 315 harmonic: 633 Sorted by residual: dihedral pdb=" CA ILE A 297 " pdb=" C ILE A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual -180.00 -164.44 -15.56 0 5.00e+00 4.00e-02 9.68e+00 dihedral pdb=" CA ILE B 297 " pdb=" C ILE B 297 " pdb=" N LYS B 298 " pdb=" CA LYS B 298 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 dihedral pdb=" CA ILE C 297 " pdb=" C ILE C 297 " pdb=" N LYS C 298 " pdb=" CA LYS C 298 " ideal model delta harmonic sigma weight residual -180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.66e+00 ... (remaining 945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 190 0.051 - 0.103: 48 0.103 - 0.154: 17 0.154 - 0.205: 3 0.205 - 0.256: 3 Chirality restraints: 261 Sorted by residual: chirality pdb=" CA LEU C 284 " pdb=" N LEU C 284 " pdb=" C LEU C 284 " pdb=" CB LEU C 284 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU B 284 " pdb=" N LEU B 284 " pdb=" C LEU B 284 " pdb=" CB LEU B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU A 284 " pdb=" N LEU A 284 " pdb=" C LEU A 284 " pdb=" CB LEU A 284 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 258 not shown) Planarity restraints: 258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 280 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C LYS C 280 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS C 280 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS C 281 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 280 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LYS A 280 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS A 280 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS A 281 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 280 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C LYS B 280 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS B 280 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B 281 " -0.008 2.00e-02 2.50e+03 ... (remaining 255 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 648 2.97 - 3.45: 1399 3.45 - 3.93: 2149 3.93 - 4.42: 2236 4.42 - 4.90: 4674 Nonbonded interactions: 11106 Sorted by model distance: nonbonded pdb=" O LEU A 284 " pdb=" O ASP C 283 " model vdw 2.482 3.040 nonbonded pdb=" O ASP A 283 " pdb=" O LEU B 284 " model vdw 2.499 3.040 nonbonded pdb=" N SER A 324 " pdb=" O GLY B 323 " model vdw 2.565 3.120 nonbonded pdb=" O GLY A 323 " pdb=" N SER C 324 " model vdw 2.578 3.120 nonbonded pdb=" N LEU A 315 " pdb=" O ASP C 314 " model vdw 2.609 3.120 ... (remaining 11101 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 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.005 0.031 1539 Z= 0.240 Angle : 0.827 7.860 2064 Z= 0.440 Chirality : 0.060 0.256 261 Planarity : 0.003 0.015 258 Dihedral : 10.782 41.305 534 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -5.74 (0.35), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.27), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.006 0.002 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.18595 ( 25) hydrogen bonds : angle 9.17720 ( 75) covalent geometry : bond 0.00470 ( 1539) covalent geometry : angle 0.82703 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 288 GLN cc_start: 0.9090 (mt0) cc_final: 0.8874 (mt0) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1605 time to fit residues: 2.8480 Evaluate side-chains 10 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS B 279 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS C 279 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101148 restraints weight = 1860.934| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.95 r_work: 0.3429 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1539 Z= 0.157 Angle : 0.617 4.013 2064 Z= 0.303 Chirality : 0.048 0.127 261 Planarity : 0.002 0.012 258 Dihedral : 5.346 15.429 219 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 9.33 % Favored : 86.67 % 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: -5.12 (0.41), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.31), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.008 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 25) hydrogen bonds : angle 5.91173 ( 75) covalent geometry : bond 0.00347 ( 1539) covalent geometry : angle 0.61711 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.166 Fit side-chains REVERT: B 293 SER cc_start: 0.9096 (p) cc_final: 0.8862 (p) REVERT: B 311 LYS cc_start: 0.8675 (mttt) cc_final: 0.8374 (mtmm) outliers start: 6 outliers final: 5 residues processed: 14 average time/residue: 0.1834 time to fit residues: 3.0182 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.109534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098705 restraints weight = 2043.888| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.05 r_work: 0.3363 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1539 Z= 0.175 Angle : 0.606 4.385 2064 Z= 0.303 Chirality : 0.048 0.125 261 Planarity : 0.002 0.014 258 Dihedral : 5.307 16.298 219 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.00 % Allowed : 10.00 % Favored : 86.00 % 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: -4.71 (0.44), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.33), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.011 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 25) hydrogen bonds : angle 5.50047 ( 75) covalent geometry : bond 0.00395 ( 1539) covalent geometry : angle 0.60628 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.165 Fit side-chains REVERT: B 311 LYS cc_start: 0.8707 (mttt) cc_final: 0.8242 (mttm) REVERT: B 317 LYS cc_start: 0.8643 (mttm) cc_final: 0.8126 (mtpt) outliers start: 6 outliers final: 6 residues processed: 13 average time/residue: 0.1969 time to fit residues: 2.9979 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.110941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.100145 restraints weight = 1890.991| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.92 r_work: 0.3447 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1539 Z= 0.135 Angle : 0.559 3.562 2064 Z= 0.278 Chirality : 0.047 0.127 261 Planarity : 0.002 0.014 258 Dihedral : 5.054 14.447 219 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.67 % Allowed : 13.33 % Favored : 82.00 % 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: -4.46 (0.45), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.34), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 TYR 0.009 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02329 ( 25) hydrogen bonds : angle 5.04630 ( 75) covalent geometry : bond 0.00301 ( 1539) covalent geometry : angle 0.55864 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.167 Fit side-chains REVERT: B 311 LYS cc_start: 0.8635 (mttt) cc_final: 0.8407 (mtmt) REVERT: B 317 LYS cc_start: 0.8540 (mttm) cc_final: 0.8020 (mtpt) outliers start: 7 outliers final: 7 residues processed: 11 average time/residue: 0.2120 time to fit residues: 2.7502 Evaluate side-chains 16 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.113412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.102276 restraints weight = 1965.771| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.09 r_work: 0.3471 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1539 Z= 0.103 Angle : 0.516 3.435 2064 Z= 0.257 Chirality : 0.047 0.127 261 Planarity : 0.002 0.014 258 Dihedral : 4.748 13.121 219 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.00 % Allowed : 14.67 % Favored : 81.33 % 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: -4.36 (0.45), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.34), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.008 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02020 ( 25) hydrogen bonds : angle 4.78476 ( 75) covalent geometry : bond 0.00229 ( 1539) covalent geometry : angle 0.51649 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.169 Fit side-chains REVERT: B 311 LYS cc_start: 0.8577 (mttt) cc_final: 0.8286 (mtmt) REVERT: B 317 LYS cc_start: 0.8483 (mttm) cc_final: 0.7960 (mtpt) outliers start: 6 outliers final: 4 residues processed: 13 average time/residue: 0.1981 time to fit residues: 3.0202 Evaluate side-chains 12 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.0170 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3692 r_free = 0.3692 target = 0.112725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101672 restraints weight = 2022.275| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.07 r_work: 0.3464 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1539 Z= 0.115 Angle : 0.527 3.392 2064 Z= 0.263 Chirality : 0.047 0.125 261 Planarity : 0.002 0.015 258 Dihedral : 4.831 13.510 219 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % 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: -4.23 (0.46), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.35), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.009 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02035 ( 25) hydrogen bonds : angle 4.80894 ( 75) covalent geometry : bond 0.00260 ( 1539) covalent geometry : angle 0.52747 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.155 Fit side-chains REVERT: B 311 LYS cc_start: 0.8616 (mttt) cc_final: 0.8355 (mtmt) REVERT: B 317 LYS cc_start: 0.8509 (mttm) cc_final: 0.8007 (mtpt) outliers start: 6 outliers final: 5 residues processed: 9 average time/residue: 0.2421 time to fit residues: 2.5487 Evaluate side-chains 13 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3575 r_free = 0.3575 target = 0.106261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095770 restraints weight = 2030.101| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.92 r_work: 0.3405 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1539 Z= 0.215 Angle : 0.642 4.322 2064 Z= 0.318 Chirality : 0.048 0.125 261 Planarity : 0.003 0.015 258 Dihedral : 5.458 16.726 219 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 4.00 % Allowed : 13.33 % Favored : 82.67 % 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: -4.25 (0.46), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.35), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.013 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 25) hydrogen bonds : angle 5.09640 ( 75) covalent geometry : bond 0.00493 ( 1539) covalent geometry : angle 0.64216 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.128 Fit side-chains REVERT: B 311 LYS cc_start: 0.8752 (mttt) cc_final: 0.8298 (mttm) REVERT: B 317 LYS cc_start: 0.8593 (mttm) cc_final: 0.8083 (mtpt) outliers start: 6 outliers final: 4 residues processed: 14 average time/residue: 0.2162 time to fit residues: 3.4827 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.110003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099272 restraints weight = 2060.636| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.04 r_work: 0.3423 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1539 Z= 0.146 Angle : 0.572 3.614 2064 Z= 0.285 Chirality : 0.047 0.125 261 Planarity : 0.002 0.016 258 Dihedral : 5.216 15.112 219 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.00 % Allowed : 15.33 % Favored : 80.67 % 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: -4.12 (0.47), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.009 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02223 ( 25) hydrogen bonds : angle 4.84251 ( 75) covalent geometry : bond 0.00334 ( 1539) covalent geometry : angle 0.57221 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.169 Fit side-chains REVERT: B 311 LYS cc_start: 0.8682 (mttt) cc_final: 0.8434 (mtmt) REVERT: B 317 LYS cc_start: 0.8528 (mttm) cc_final: 0.7999 (mtpt) outliers start: 6 outliers final: 6 residues processed: 13 average time/residue: 0.2303 time to fit residues: 3.4414 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.106034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095470 restraints weight = 2019.023| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.90 r_work: 0.3390 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1539 Z= 0.219 Angle : 0.650 4.304 2064 Z= 0.322 Chirality : 0.048 0.124 261 Planarity : 0.003 0.017 258 Dihedral : 5.559 16.967 219 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 4.67 % Allowed : 14.67 % Favored : 80.67 % 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: -4.17 (0.47), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.36), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.012 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02785 ( 25) hydrogen bonds : angle 5.14163 ( 75) covalent geometry : bond 0.00504 ( 1539) covalent geometry : angle 0.64999 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.158 Fit side-chains REVERT: B 311 LYS cc_start: 0.8750 (mttt) cc_final: 0.8304 (mttm) REVERT: B 317 LYS cc_start: 0.8592 (mttm) cc_final: 0.8079 (mtpt) outliers start: 7 outliers final: 5 residues processed: 14 average time/residue: 0.2723 time to fit residues: 4.2742 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.109301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098210 restraints weight = 2131.604| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.15 r_work: 0.3414 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1539 Z= 0.150 Angle : 0.577 3.554 2064 Z= 0.287 Chirality : 0.047 0.125 261 Planarity : 0.002 0.018 258 Dihedral : 5.285 15.167 219 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.67 % Allowed : 14.67 % Favored : 80.67 % 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: -4.03 (0.48), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.009 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02198 ( 25) hydrogen bonds : angle 4.90931 ( 75) covalent geometry : bond 0.00345 ( 1539) covalent geometry : angle 0.57749 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.177 Fit side-chains REVERT: B 311 LYS cc_start: 0.8696 (mttt) cc_final: 0.8400 (mtmt) REVERT: B 317 LYS cc_start: 0.8535 (mttm) cc_final: 0.8009 (mtpt) outliers start: 7 outliers final: 6 residues processed: 15 average time/residue: 0.2648 time to fit residues: 4.4540 Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.112053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100851 restraints weight = 2072.721| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.13 r_work: 0.3470 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1539 Z= 0.101 Angle : 0.516 3.329 2064 Z= 0.257 Chirality : 0.047 0.128 261 Planarity : 0.002 0.020 258 Dihedral : 4.872 13.095 219 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.67 % Allowed : 16.67 % Favored : 80.67 % 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: -3.91 (0.48), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.007 0.002 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.01769 ( 25) hydrogen bonds : angle 4.66845 ( 75) covalent geometry : bond 0.00230 ( 1539) covalent geometry : angle 0.51628 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.29 seconds wall clock time: 24 minutes 50.39 seconds (1490.39 seconds total)