Starting phenix.real_space_refine on Thu Jul 31 05:16:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyf_29572/07_2025/8fyf_29572.cif" } resolution = 3.4 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= 0.003 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4244 2.51 5 N 1086 2.21 5 O 1080 1.98 5 H 6754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 8.47, per 1000 atoms: 0.64 Number of scatterers: 13202 At special positions: 0 Unit cell: (105.25, 73.254, 82.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1080 8.00 N 1086 7.00 C 4244 6.00 H 6754 1.00 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: 3.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 89.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.882A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.701A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.881A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.910A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.566A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.500A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.886A pdb=" N ARG B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.699A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.856A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.911A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.567A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'D' and resid 384 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.266A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.287A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1545 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: 4.83 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6736 1.03 - 1.23: 20 1.23 - 1.42: 2680 1.42 - 1.61: 3852 1.61 - 1.81: 58 Bond restraints: 13346 Sorted by residual: bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.27e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.12e+00 bond pdb=" N LEU C 383 " pdb=" CA LEU C 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N LEU D 383 " pdb=" CA LEU D 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 13341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 23336 1.34 - 2.68: 794 2.68 - 4.02: 58 4.02 - 5.36: 12 5.36 - 6.71: 2 Bond angle restraints: 24202 Sorted by residual: angle pdb=" N GLU A 403 " pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 114.56 111.34 3.22 1.27e+00 6.20e-01 6.45e+00 angle pdb=" N GLU B 403 " pdb=" CA GLU B 403 " pdb=" C GLU B 403 " ideal model delta sigma weight residual 114.56 111.36 3.20 1.27e+00 6.20e-01 6.35e+00 angle pdb=" C ILE A 60 " pdb=" N SER A 61 " pdb=" CA SER A 61 " ideal model delta sigma weight residual 122.00 119.39 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 108.55 112.86 -4.31 1.79e+00 3.12e-01 5.81e+00 angle pdb=" C ILE B 60 " pdb=" N SER B 61 " pdb=" CA SER B 61 " ideal model delta sigma weight residual 122.00 119.43 2.57 1.08e+00 8.57e-01 5.66e+00 ... (remaining 24197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5611 17.62 - 35.23: 459 35.23 - 52.85: 127 52.85 - 70.47: 43 70.47 - 88.09: 8 Dihedral angle restraints: 6248 sinusoidal: 3352 harmonic: 2896 Sorted by residual: dihedral pdb=" CA GLU A 59 " pdb=" C GLU A 59 " pdb=" N ILE A 60 " pdb=" CA ILE A 60 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU B 59 " pdb=" C GLU B 59 " pdb=" N ILE B 60 " pdb=" CA ILE B 60 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 716 0.028 - 0.055: 235 0.055 - 0.083: 109 0.083 - 0.111: 36 0.111 - 0.138: 10 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1103 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 254 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO B 255 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 288 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 288 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.019 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 203 2.08 - 2.71: 21938 2.71 - 3.34: 39930 3.34 - 3.97: 47602 3.97 - 4.60: 76240 Nonbonded interactions: 185913 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.451 2.450 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.452 2.450 nonbonded pdb=" OE1 GLN A 171 " pdb=" H GLN A 171 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLN B 171 " pdb=" H GLN B 171 " model vdw 1.637 2.450 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.666 2.450 ... (remaining 185908 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.190 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.003 0.033 6592 Z= 0.152 Angle : 0.582 6.706 8974 Z= 0.331 Chirality : 0.036 0.138 1106 Planarity : 0.004 0.034 1098 Dihedral : 14.089 88.087 2318 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.30), residues: 818 helix: 2.32 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.24 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.011 0.001 PHE B 314 TYR 0.008 0.001 TYR A 313 ARG 0.002 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.11443 ( 523) hydrogen bonds : angle 4.80284 ( 1545) covalent geometry : bond 0.00292 ( 6592) covalent geometry : angle 0.58153 ( 8974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.051 Fit side-chains REVERT: B 426 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7217 (t80) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3682 time to fit residues: 38.4351 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.125727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095482 restraints weight = 32605.136| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.42 r_work: 0.2955 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6592 Z= 0.148 Angle : 0.546 5.006 8974 Z= 0.296 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.885 49.427 892 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.86 % Allowed : 10.92 % Favored : 88.22 % 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: 2.89 (0.30), residues: 818 helix: 2.30 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.52 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 449 PHE 0.010 0.001 PHE A 164 TYR 0.010 0.001 TYR A 160 ARG 0.001 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 523) hydrogen bonds : angle 4.39438 ( 1545) covalent geometry : bond 0.00310 ( 6592) covalent geometry : angle 0.54635 ( 8974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.141 Fit side-chains REVERT: A 65 GLN cc_start: 0.3491 (OUTLIER) cc_final: 0.2732 (tm-30) REVERT: A 284 ASN cc_start: 0.8209 (t0) cc_final: 0.8005 (m-40) REVERT: A 293 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 426 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 65 GLN cc_start: 0.3483 (OUTLIER) cc_final: 0.2725 (tm-30) REVERT: B 284 ASN cc_start: 0.8229 (t0) cc_final: 0.8022 (m-40) REVERT: B 293 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: B 426 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7269 (t80) outliers start: 6 outliers final: 0 residues processed: 81 average time/residue: 0.3787 time to fit residues: 42.7686 Evaluate side-chains 78 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.093662 restraints weight = 32890.110| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.48 r_work: 0.2932 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6592 Z= 0.177 Angle : 0.548 5.009 8974 Z= 0.294 Chirality : 0.037 0.109 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.889 49.744 892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.15 % Allowed : 10.78 % Favored : 88.07 % 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: 2.88 (0.30), residues: 818 helix: 2.36 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.69 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS B 328 PHE 0.011 0.001 PHE B 264 TYR 0.009 0.001 TYR B 313 ARG 0.001 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.05205 ( 523) hydrogen bonds : angle 4.28988 ( 1545) covalent geometry : bond 0.00386 ( 6592) covalent geometry : angle 0.54752 ( 8974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.231 Fit side-chains REVERT: A 65 GLN cc_start: 0.3435 (OUTLIER) cc_final: 0.2718 (tm-30) REVERT: A 284 ASN cc_start: 0.8245 (t0) cc_final: 0.8012 (m-40) REVERT: A 293 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 426 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.7329 (t80) REVERT: B 65 GLN cc_start: 0.3432 (OUTLIER) cc_final: 0.2711 (tm-30) REVERT: B 284 ASN cc_start: 0.8260 (t0) cc_final: 0.8021 (m-40) REVERT: B 293 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: B 426 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.7203 (t80) outliers start: 8 outliers final: 2 residues processed: 85 average time/residue: 0.3361 time to fit residues: 39.8115 Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097631 restraints weight = 32198.552| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.34 r_work: 0.2981 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.118 Angle : 0.508 4.943 8974 Z= 0.270 Chirality : 0.035 0.110 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.767 50.618 892 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 10.63 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.30), residues: 818 helix: 2.63 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.70 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS B 57 PHE 0.008 0.001 PHE A 99 TYR 0.009 0.001 TYR A 313 ARG 0.002 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 523) hydrogen bonds : angle 4.07736 ( 1545) covalent geometry : bond 0.00243 ( 6592) covalent geometry : angle 0.50829 ( 8974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.997 Fit side-chains REVERT: A 65 GLN cc_start: 0.3587 (OUTLIER) cc_final: 0.2953 (tm-30) REVERT: A 284 ASN cc_start: 0.8195 (t0) cc_final: 0.7984 (m-40) REVERT: A 293 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 426 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7403 (t80) REVERT: B 65 GLN cc_start: 0.3586 (OUTLIER) cc_final: 0.2949 (tm-30) REVERT: B 284 ASN cc_start: 0.8206 (t0) cc_final: 0.7992 (m-40) REVERT: B 293 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 426 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.7289 (t80) outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 0.3473 time to fit residues: 39.9395 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.124819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093430 restraints weight = 32872.144| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.50 r_work: 0.2944 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.198 Angle : 0.546 4.977 8974 Z= 0.294 Chirality : 0.037 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.834 50.017 892 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 11.06 % Favored : 87.36 % 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: 2.98 (0.30), residues: 818 helix: 2.45 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.77 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.002 PHE A 99 TYR 0.009 0.001 TYR B 313 ARG 0.002 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 523) hydrogen bonds : angle 4.17408 ( 1545) covalent geometry : bond 0.00442 ( 6592) covalent geometry : angle 0.54561 ( 8974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.805 Fit side-chains REVERT: A 65 GLN cc_start: 0.3444 (OUTLIER) cc_final: 0.2767 (tm-30) REVERT: A 284 ASN cc_start: 0.8225 (t0) cc_final: 0.7980 (m-40) REVERT: A 293 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 426 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 65 GLN cc_start: 0.3454 (OUTLIER) cc_final: 0.2759 (tm-30) REVERT: B 284 ASN cc_start: 0.8221 (t0) cc_final: 0.7980 (m-40) REVERT: B 293 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7122 (mp0) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.4327 time to fit residues: 54.6380 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094643 restraints weight = 32919.246| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.51 r_work: 0.2944 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6592 Z= 0.133 Angle : 0.511 4.943 8974 Z= 0.272 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.749 50.645 892 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.30 % Allowed : 10.92 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.30), residues: 818 helix: 2.59 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.83 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.003 0.001 HIS A 328 PHE 0.009 0.001 PHE A 99 TYR 0.009 0.001 TYR B 313 ARG 0.001 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 523) hydrogen bonds : angle 4.05651 ( 1545) covalent geometry : bond 0.00287 ( 6592) covalent geometry : angle 0.51074 ( 8974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3425 (OUTLIER) cc_final: 0.2719 (tm-30) REVERT: A 284 ASN cc_start: 0.8229 (t0) cc_final: 0.7958 (m-40) REVERT: A 293 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 426 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.7346 (t80) REVERT: B 65 GLN cc_start: 0.3422 (OUTLIER) cc_final: 0.2716 (tm-30) REVERT: B 284 ASN cc_start: 0.8229 (t0) cc_final: 0.7951 (m-40) REVERT: B 293 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: B 426 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.7232 (t80) outliers start: 16 outliers final: 7 residues processed: 88 average time/residue: 0.4191 time to fit residues: 49.3860 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097352 restraints weight = 32309.867| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.37 r_work: 0.2972 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6592 Z= 0.119 Angle : 0.507 4.885 8974 Z= 0.272 Chirality : 0.035 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.710 50.890 892 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.87 % Allowed : 10.92 % Favored : 87.21 % 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: 3.34 (0.30), residues: 818 helix: 2.72 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.89 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.015 0.001 HIS A 177 PHE 0.009 0.001 PHE A 99 TYR 0.009 0.001 TYR B 313 ARG 0.003 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 523) hydrogen bonds : angle 4.00570 ( 1545) covalent geometry : bond 0.00249 ( 6592) covalent geometry : angle 0.50738 ( 8974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3563 (OUTLIER) cc_final: 0.2895 (tm-30) REVERT: A 284 ASN cc_start: 0.8172 (t0) cc_final: 0.7947 (m-40) REVERT: A 293 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 426 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.7354 (t80) REVERT: B 65 GLN cc_start: 0.3549 (OUTLIER) cc_final: 0.2884 (tm-30) REVERT: B 284 ASN cc_start: 0.8189 (t0) cc_final: 0.7961 (m-40) REVERT: B 293 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: B 426 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.7222 (t80) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.4721 time to fit residues: 53.8083 Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.126185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096565 restraints weight = 32522.435| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.41 r_work: 0.2970 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6592 Z= 0.132 Angle : 0.505 4.893 8974 Z= 0.270 Chirality : 0.036 0.112 1106 Planarity : 0.004 0.034 1098 Dihedral : 4.659 50.808 892 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 10.49 % Favored : 87.79 % 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 (0.30), residues: 818 helix: 2.74 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.88 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.012 0.001 HIS B 177 PHE 0.009 0.001 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.001 0.000 ARG B 174 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 523) hydrogen bonds : angle 3.93814 ( 1545) covalent geometry : bond 0.00286 ( 6592) covalent geometry : angle 0.50505 ( 8974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.215 Fit side-chains REVERT: A 65 GLN cc_start: 0.3601 (OUTLIER) cc_final: 0.2903 (tm-30) REVERT: A 293 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 426 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.7351 (t80) REVERT: B 65 GLN cc_start: 0.3603 (OUTLIER) cc_final: 0.2900 (tm-30) REVERT: B 293 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 426 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7203 (t80) outliers start: 12 outliers final: 4 residues processed: 84 average time/residue: 0.4171 time to fit residues: 46.7923 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093607 restraints weight = 32592.585| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.47 r_work: 0.2960 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6592 Z= 0.187 Angle : 0.541 5.175 8974 Z= 0.291 Chirality : 0.037 0.111 1106 Planarity : 0.004 0.034 1098 Dihedral : 4.734 50.365 892 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.72 % Allowed : 10.63 % Favored : 87.64 % 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: 3.07 (0.30), residues: 818 helix: 2.54 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.002 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.002 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 523) hydrogen bonds : angle 4.04749 ( 1545) covalent geometry : bond 0.00418 ( 6592) covalent geometry : angle 0.54149 ( 8974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.095 Fit side-chains REVERT: A 65 GLN cc_start: 0.3508 (OUTLIER) cc_final: 0.2656 (tm-30) REVERT: A 293 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 65 GLN cc_start: 0.3428 (OUTLIER) cc_final: 0.2576 (tm-30) REVERT: B 293 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7081 (mp0) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.3961 time to fit residues: 44.4523 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.124507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.093103 restraints weight = 32721.205| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.49 r_work: 0.2993 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 6592 Z= 0.357 Angle : 1.233 59.200 8974 Z= 0.765 Chirality : 0.037 0.165 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.741 50.407 892 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.44 % Allowed : 10.34 % Favored : 88.22 % Cbeta Deviations : 0.25 % 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: 3.07 (0.30), residues: 818 helix: 2.54 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.001 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.001 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 523) hydrogen bonds : angle 4.01964 ( 1545) covalent geometry : bond 0.00715 ( 6592) covalent geometry : angle 1.23277 ( 8974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.219 Fit side-chains REVERT: A 65 GLN cc_start: 0.3506 (OUTLIER) cc_final: 0.2655 (tm-30) REVERT: A 293 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: B 65 GLN cc_start: 0.3423 (OUTLIER) cc_final: 0.2573 (tm-30) REVERT: B 293 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7079 (mp0) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.5066 time to fit residues: 57.2839 Evaluate side-chains 80 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.093215 restraints weight = 32824.963| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.48 r_work: 0.2965 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 6592 Z= 0.357 Angle : 1.233 59.200 8974 Z= 0.765 Chirality : 0.037 0.165 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.741 50.407 892 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.44 % Allowed : 10.49 % Favored : 88.07 % Cbeta Deviations : 0.25 % 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: 3.07 (0.30), residues: 818 helix: 2.54 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.001 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.001 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 523) hydrogen bonds : angle 4.01964 ( 1545) covalent geometry : bond 0.00715 ( 6592) covalent geometry : angle 1.23277 ( 8974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5980.88 seconds wall clock time: 109 minutes 10.98 seconds (6550.98 seconds total)