Starting phenix.real_space_refine on Tue Feb 11 14:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtn_24684/02_2025/7rtn_24684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtn_24684/02_2025/7rtn_24684.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/7rtn_24684/02_2025/7rtn_24684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtn_24684/02_2025/7rtn_24684.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtn_24684/02_2025/7rtn_24684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtn_24684/02_2025/7rtn_24684.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= 0.002 sd= 0.008 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 12 5.16 5 C 3792 2.51 5 N 1098 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 4.70, per 1000 atoms: 0.78 Number of scatterers: 6018 At special positions: 0 Unit cell: (104.72, 104.72, 111.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1116 8.00 N 1098 7.00 C 3792 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: 1.60 Conformation dependent library (CDL) restraints added in 857.9 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 56.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.967A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.719A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.982A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.911A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'B' and resid 65 through 79 removed outlier: 4.009A pdb=" N LYS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 135 removed outlier: 3.531A pdb=" N ARG B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 removed outlier: 3.970A pdb=" N GLY B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.755A pdb=" N PHE B 354 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 355 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 438 removed outlier: 3.550A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.953A pdb=" N THR B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 3.501A pdb=" N ARG C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.037A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.843A pdb=" N VAL C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.838A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.586A pdb=" N ARG C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 5.696A pdb=" N ILE A 364 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 463 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 366 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 463 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL B 366 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 6.421A pdb=" N ILE C 364 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C 463 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 366 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 408 hydrogen bonds defined for protein. 1176 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: 1.65 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.46: 1019 1.46 - 1.58: 3022 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 6144 Sorted by residual: bond pdb=" CG LYS B 98 " pdb=" CD LYS B 98 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.08e+00 bond pdb=" CB GLU C 82 " pdb=" CG GLU C 82 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CG GLU C 82 " pdb=" CD GLU C 82 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.25e-01 bond pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 7.98e-01 ... (remaining 6139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8200 2.00 - 3.99: 123 3.99 - 5.99: 11 5.99 - 7.99: 7 7.99 - 9.99: 2 Bond angle restraints: 8343 Sorted by residual: angle pdb=" C THR C 443 " pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C THR B 443 " pdb=" N GLN B 444 " pdb=" CA GLN B 444 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C HIS C 384 " pdb=" N HIS C 385 " pdb=" CA HIS C 385 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LEU B 414 " pdb=" CB LEU B 414 " pdb=" CG LEU B 414 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.14e+00 angle pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " pdb=" CG GLN C 444 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.36e+00 ... (remaining 8338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3244 17.84 - 35.68: 311 35.68 - 53.52: 55 53.52 - 71.36: 10 71.36 - 89.19: 4 Dihedral angle restraints: 3624 sinusoidal: 1284 harmonic: 2340 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual 180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA HIS B 385 " pdb=" C HIS B 385 " pdb=" N HIS B 386 " pdb=" CA HIS B 386 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 584 0.035 - 0.070: 249 0.070 - 0.105: 70 0.105 - 0.139: 25 0.139 - 0.174: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CB ILE B 399 " pdb=" CA ILE B 399 " pdb=" CG1 ILE B 399 " pdb=" CG2 ILE B 399 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CG LEU C 433 " pdb=" CB LEU C 433 " pdb=" CD1 LEU C 433 " pdb=" CD2 LEU C 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 89 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C 90 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 89 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 90 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.013 2.00e-02 2.50e+03 9.35e-03 1.53e+00 pdb=" CG PHE C 378 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.005 2.00e-02 2.50e+03 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1748 2.82 - 3.34: 5705 3.34 - 3.86: 9613 3.86 - 4.38: 10615 4.38 - 4.90: 18932 Nonbonded interactions: 46613 Sorted by model distance: nonbonded pdb=" O ALA B 369 " pdb=" OG SER B 373 " model vdw 2.298 3.040 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.311 3.120 nonbonded pdb=" O HIS B 384 " pdb=" ND1 HIS B 385 " model vdw 2.317 3.120 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.351 3.040 nonbonded pdb=" OD2 ASP C 86 " pdb=" NH2 ARG C 499 " model vdw 2.353 3.120 ... (remaining 46608 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.070 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.004 0.045 6144 Z= 0.237 Angle : 0.631 9.986 8343 Z= 0.333 Chirality : 0.044 0.174 930 Planarity : 0.004 0.036 1107 Dihedral : 14.578 89.195 2112 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.60 (0.31), residues: 798 helix: 1.96 (0.25), residues: 423 sheet: -0.01 (0.44), residues: 139 loop : -2.36 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.008 0.001 HIS B 489 PHE 0.020 0.002 PHE C 378 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1832 time to fit residues: 28.0111 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147593 restraints weight = 9461.605| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.20 r_work: 0.3541 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6144 Z= 0.168 Angle : 0.546 8.375 8343 Z= 0.289 Chirality : 0.041 0.152 930 Planarity : 0.003 0.031 1107 Dihedral : 4.171 20.613 870 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % Favored : 87.57 % 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: 0.88 (0.31), residues: 798 helix: 2.22 (0.25), residues: 438 sheet: 0.15 (0.46), residues: 136 loop : -2.63 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 371 HIS 0.005 0.001 HIS B 385 PHE 0.019 0.002 PHE C 378 TYR 0.011 0.001 TYR A 367 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.696 Fit side-chains REVERT: A 400 ASP cc_start: 0.7138 (t0) cc_final: 0.6877 (t0) REVERT: A 438 SER cc_start: 0.8439 (m) cc_final: 0.8032 (p) REVERT: B 92 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8011 (mt-10) REVERT: B 482 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7220 (p90) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.1562 time to fit residues: 20.3944 Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142717 restraints weight = 9681.883| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.24 r_work: 0.3488 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6144 Z= 0.321 Angle : 0.612 9.216 8343 Z= 0.326 Chirality : 0.043 0.151 930 Planarity : 0.004 0.037 1107 Dihedral : 4.718 22.101 870 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.70 % Allowed : 11.35 % Favored : 85.95 % 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: 0.75 (0.31), residues: 798 helix: 2.10 (0.25), residues: 433 sheet: 0.01 (0.45), residues: 133 loop : -2.45 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 371 HIS 0.009 0.002 HIS B 385 PHE 0.021 0.002 PHE A 378 TYR 0.014 0.002 TYR A 367 ARG 0.004 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.631 Fit side-chains REVERT: A 400 ASP cc_start: 0.7196 (t0) cc_final: 0.6961 (t0) REVERT: A 405 GLU cc_start: 0.8005 (tt0) cc_final: 0.7760 (tt0) REVERT: B 92 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8090 (mt-10) REVERT: B 482 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7321 (p90) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.1511 time to fit residues: 20.1977 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.172727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148462 restraints weight = 9714.010| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.05 r_work: 0.3503 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6144 Z= 0.269 Angle : 0.578 8.458 8343 Z= 0.308 Chirality : 0.042 0.139 930 Planarity : 0.004 0.037 1107 Dihedral : 4.571 21.711 870 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.60 % Allowed : 14.23 % Favored : 82.16 % 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: 0.77 (0.31), residues: 798 helix: 2.11 (0.25), residues: 433 sheet: 0.06 (0.46), residues: 133 loop : -2.45 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.013 0.001 TYR A 367 ARG 0.003 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.691 Fit side-chains REVERT: A 400 ASP cc_start: 0.7182 (t0) cc_final: 0.6868 (t0) REVERT: B 92 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7968 (mt-10) REVERT: B 482 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7304 (p90) REVERT: B 489 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8509 (m170) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.1527 time to fit residues: 21.1645 Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 40.0000 chunk 55 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148401 restraints weight = 9719.679| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.94 r_work: 0.3538 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6144 Z= 0.236 Angle : 0.570 8.467 8343 Z= 0.302 Chirality : 0.042 0.148 930 Planarity : 0.004 0.036 1107 Dihedral : 4.452 21.271 870 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.96 % Allowed : 15.50 % Favored : 80.54 % 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: 0.88 (0.31), residues: 798 helix: 2.19 (0.25), residues: 433 sheet: -0.02 (0.45), residues: 139 loop : -2.34 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.012 0.001 TYR A 367 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.743 Fit side-chains REVERT: A 400 ASP cc_start: 0.7134 (t0) cc_final: 0.6798 (t0) REVERT: B 92 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8015 (mt-10) REVERT: B 105 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: B 482 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7264 (p90) REVERT: B 489 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8462 (m170) outliers start: 22 outliers final: 16 residues processed: 98 average time/residue: 0.1478 time to fit residues: 20.1990 Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 36 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS C 465 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.168960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146098 restraints weight = 9602.271| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.58 r_work: 0.3460 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6144 Z= 0.437 Angle : 0.689 9.011 8343 Z= 0.369 Chirality : 0.046 0.183 930 Planarity : 0.005 0.039 1107 Dihedral : 5.155 23.064 870 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.14 % Allowed : 16.58 % Favored : 79.28 % 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: 0.35 (0.30), residues: 798 helix: 1.66 (0.25), residues: 432 sheet: -0.01 (0.46), residues: 133 loop : -2.45 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.011 0.002 HIS B 385 PHE 0.023 0.003 PHE C 497 TYR 0.018 0.002 TYR A 367 ARG 0.005 0.001 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.629 Fit side-chains REVERT: A 115 TYR cc_start: 0.3003 (OUTLIER) cc_final: 0.2649 (t80) REVERT: A 385 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7027 (p-80) REVERT: B 92 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7776 (mt-10) REVERT: B 105 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: B 482 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7345 (p90) REVERT: B 489 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8671 (m170) REVERT: C 485 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7026 (tm-30) outliers start: 23 outliers final: 17 residues processed: 100 average time/residue: 0.1558 time to fit residues: 21.1868 Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 51 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS B 457 HIS C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146873 restraints weight = 9611.696| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.94 r_work: 0.3542 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6144 Z= 0.205 Angle : 0.569 8.611 8343 Z= 0.301 Chirality : 0.041 0.138 930 Planarity : 0.004 0.037 1107 Dihedral : 4.492 21.126 870 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.78 % Allowed : 18.38 % Favored : 77.84 % 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: 0.88 (0.31), residues: 798 helix: 2.14 (0.25), residues: 432 sheet: 0.12 (0.46), residues: 136 loop : -2.28 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.021 0.002 PHE C 392 TYR 0.012 0.001 TYR A 367 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.664 Fit side-chains REVERT: A 115 TYR cc_start: 0.3247 (OUTLIER) cc_final: 0.2996 (t80) REVERT: A 385 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.6972 (p-80) REVERT: A 438 SER cc_start: 0.8315 (m) cc_final: 0.7958 (p) REVERT: B 92 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8091 (mt-10) REVERT: B 105 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: B 482 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7228 (p90) REVERT: B 489 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8265 (m170) REVERT: C 485 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7276 (tm-30) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.1548 time to fit residues: 21.5952 Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147675 restraints weight = 9556.350| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.02 r_work: 0.3540 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6144 Z= 0.205 Angle : 0.561 8.462 8343 Z= 0.297 Chirality : 0.041 0.142 930 Planarity : 0.004 0.038 1107 Dihedral : 4.405 21.442 870 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.96 % Allowed : 18.38 % Favored : 77.66 % 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: 1.01 (0.31), residues: 798 helix: 2.29 (0.25), residues: 435 sheet: 0.19 (0.46), residues: 136 loop : -2.40 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.020 0.002 PHE C 392 TYR 0.012 0.001 TYR A 367 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.635 Fit side-chains REVERT: A 115 TYR cc_start: 0.3197 (OUTLIER) cc_final: 0.2726 (t80) REVERT: A 385 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6858 (p-80) REVERT: A 438 SER cc_start: 0.8368 (m) cc_final: 0.7997 (p) REVERT: B 92 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8084 (mt-10) REVERT: B 105 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: B 482 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7208 (p90) REVERT: B 489 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8196 (m170) REVERT: C 103 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: C 485 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7262 (tm-30) outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 0.1684 time to fit residues: 22.7138 Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149139 restraints weight = 9553.889| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.30 r_work: 0.3559 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6144 Z= 0.164 Angle : 0.539 8.325 8343 Z= 0.284 Chirality : 0.040 0.152 930 Planarity : 0.003 0.038 1107 Dihedral : 4.115 21.215 870 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.78 % Allowed : 18.38 % Favored : 77.84 % 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: 1.28 (0.31), residues: 798 helix: 2.47 (0.25), residues: 437 sheet: 0.89 (0.49), residues: 121 loop : -2.47 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 371 HIS 0.008 0.001 HIS B 385 PHE 0.021 0.002 PHE C 392 TYR 0.009 0.001 TYR A 367 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.535 Fit side-chains REVERT: A 115 TYR cc_start: 0.2794 (OUTLIER) cc_final: 0.2246 (t80) REVERT: A 385 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.6856 (p-80) REVERT: A 438 SER cc_start: 0.8168 (m) cc_final: 0.7837 (p) REVERT: B 105 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: B 482 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6805 (p90) REVERT: B 489 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8139 (m-70) REVERT: C 103 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6498 (tm-30) outliers start: 21 outliers final: 13 residues processed: 103 average time/residue: 0.1397 time to fit residues: 20.3556 Evaluate side-chains 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS ** C 386 HIS ** 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 = 0.3996 r_free = 0.3996 target = 0.173891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148821 restraints weight = 9659.123| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.16 r_work: 0.3539 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6144 Z= 0.168 Angle : 0.538 8.046 8343 Z= 0.283 Chirality : 0.040 0.159 930 Planarity : 0.004 0.037 1107 Dihedral : 4.133 23.968 870 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.42 % Allowed : 18.38 % Favored : 78.20 % 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: 1.31 (0.31), residues: 798 helix: 2.51 (0.24), residues: 436 sheet: 0.76 (0.49), residues: 124 loop : -2.41 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.021 0.002 PHE C 392 TYR 0.011 0.001 TYR A 367 ARG 0.004 0.000 ARG B 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.628 Fit side-chains REVERT: A 115 TYR cc_start: 0.3016 (OUTLIER) cc_final: 0.2432 (t80) REVERT: A 385 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.6972 (p-80) REVERT: B 105 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: B 482 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6875 (p90) REVERT: B 489 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8179 (m-70) REVERT: C 103 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6541 (tm-30) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 0.1444 time to fit residues: 19.3167 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS ** C 386 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.172439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147251 restraints weight = 9680.519| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.33 r_work: 0.3517 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6144 Z= 0.246 Angle : 0.575 7.970 8343 Z= 0.305 Chirality : 0.042 0.163 930 Planarity : 0.004 0.037 1107 Dihedral : 4.468 25.037 870 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.42 % Allowed : 18.38 % Favored : 78.20 % 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: 1.13 (0.31), residues: 798 helix: 2.33 (0.25), residues: 437 sheet: 0.33 (0.47), residues: 134 loop : -2.31 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 371 HIS 0.011 0.001 HIS B 385 PHE 0.019 0.002 PHE C 392 TYR 0.013 0.001 TYR A 367 ARG 0.004 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.64 seconds wall clock time: 58 minutes 42.31 seconds (3522.31 seconds total)