Starting phenix.real_space_refine on Tue Mar 11 14:29:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtn_24684/03_2025/7rtn_24684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtn_24684/03_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_24684/03_2025/7rtn_24684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2025/7rtn_24684.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_2025/7rtn_24684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtn_24684/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.34, per 1000 atoms: 0.89 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: 1.64 Conformation dependent library (CDL) restraints added in 908.9 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: 0.62 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: 1.73 Time building geometry restraints manager: 1.92 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: 0.010 Normalize map: mean=0, sd=1: 1.160 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.220 Find NCS groups from input model: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- 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 : 0.666 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1772 time to fit residues: 27.3582 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 : 0.657 ------------------------------------------------------------------------------- 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 = 0.147584 restraints weight = 9461.614| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.20 r_work: 0.3545 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.684 Fit side-chains REVERT: A 400 ASP cc_start: 0.7128 (t0) cc_final: 0.6865 (t0) REVERT: A 438 SER cc_start: 0.8446 (m) cc_final: 0.8040 (p) REVERT: B 92 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8001 (mt-10) REVERT: B 482 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7214 (p90) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.1485 time to fit residues: 19.4296 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 : 0.780 ------------------------------------------------------------------------------- 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: 10.0000 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: 20.0000 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.168599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141935 restraints weight = 9680.881| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.26 r_work: 0.3472 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6144 Z= 0.373 Angle : 0.641 9.150 8343 Z= 0.343 Chirality : 0.044 0.167 930 Planarity : 0.004 0.038 1107 Dihedral : 4.915 22.537 870 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.70 % Allowed : 12.07 % Favored : 85.23 % 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: 0.59 (0.31), residues: 798 helix: 1.95 (0.25), residues: 432 sheet: -0.04 (0.45), residues: 133 loop : -2.46 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.010 0.002 HIS B 385 PHE 0.022 0.003 PHE A 378 TYR 0.015 0.002 TYR A 367 ARG 0.005 0.001 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 : 0.660 Fit side-chains REVERT: A 405 GLU cc_start: 0.8044 (tt0) cc_final: 0.7800 (tt0) REVERT: B 92 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7910 (mt-10) REVERT: B 482 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7304 (p90) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.1516 time to fit residues: 20.5345 Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 9.9990 chunk 63 optimal weight: 50.0000 chunk 70 optimal weight: 0.0070 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.174261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148090 restraints weight = 9697.078| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.99 r_work: 0.3531 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6144 Z= 0.193 Angle : 0.544 8.486 8343 Z= 0.289 Chirality : 0.041 0.135 930 Planarity : 0.004 0.035 1107 Dihedral : 4.319 20.980 870 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.24 % Allowed : 14.59 % 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: 0.94 (0.31), residues: 798 helix: 2.28 (0.25), residues: 432 sheet: 0.09 (0.44), residues: 139 loop : -2.44 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.008 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.023 0.001 TYR A 466 ARG 0.002 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 112 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.617 Fit side-chains REVERT: A 438 SER cc_start: 0.8349 (m) cc_final: 0.7997 (p) REVERT: B 92 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8095 (mt-10) REVERT: B 482 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7090 (p90) REVERT: B 489 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8344 (m170) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.1469 time to fit residues: 21.5852 Evaluate side-chains 97 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 B residue 489 HIS 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: 10.0000 chunk 59 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.173590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147524 restraints weight = 9697.325| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.95 r_work: 0.3562 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1403 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= 0.217 Angle : 0.562 8.393 8343 Z= 0.296 Chirality : 0.041 0.148 930 Planarity : 0.003 0.036 1107 Dihedral : 4.336 20.990 870 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.78 % Allowed : 15.86 % Favored : 80.36 % 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: 0.93 (0.31), residues: 798 helix: 2.30 (0.25), residues: 431 sheet: -0.00 (0.44), residues: 142 loop : -2.45 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.010 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 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.644 Fit side-chains REVERT: A 438 SER cc_start: 0.8369 (m) cc_final: 0.8008 (p) REVERT: B 92 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8115 (mt-10) REVERT: B 105 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: B 482 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7185 (p90) REVERT: B 489 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8323 (m170) REVERT: C 103 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6496 (tm-30) outliers start: 21 outliers final: 14 residues processed: 96 average time/residue: 0.1372 time to fit residues: 18.7207 Evaluate side-chains 101 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 58 optimal weight: 30.0000 chunk 60 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 overall best weight: 6.4388 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146161 restraints weight = 9537.679| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.15 r_work: 0.3502 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6144 Z= 0.248 Angle : 0.575 8.319 8343 Z= 0.305 Chirality : 0.042 0.143 930 Planarity : 0.004 0.035 1107 Dihedral : 4.447 21.249 870 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.96 % Allowed : 16.22 % Favored : 79.82 % 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: 0.87 (0.31), residues: 798 helix: 2.22 (0.25), residues: 433 sheet: -0.03 (0.44), residues: 142 loop : -2.47 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 PHE 0.019 0.002 PHE A 378 TYR 0.012 0.001 TYR A 367 ARG 0.003 0.000 ARG C 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 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.621 Fit side-chains REVERT: A 385 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6762 (p-80) REVERT: B 92 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7839 (mt-10) REVERT: B 105 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 482 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7222 (p90) REVERT: B 489 HIS cc_start: 0.8792 (OUTLIER) cc_final: 0.8336 (m170) REVERT: C 103 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: C 485 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7056 (tm-30) outliers start: 22 outliers final: 16 residues processed: 101 average time/residue: 0.1339 time to fit residues: 19.2260 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 65 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.0484 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.175633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151085 restraints weight = 9547.410| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.93 r_work: 0.3563 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1614 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= 0.158 Angle : 0.532 8.433 8343 Z= 0.280 Chirality : 0.040 0.131 930 Planarity : 0.003 0.036 1107 Dihedral : 4.093 20.216 870 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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: 1.23 (0.31), residues: 798 helix: 2.47 (0.25), residues: 432 sheet: 0.83 (0.48), residues: 121 loop : -2.43 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 371 HIS 0.008 0.001 HIS B 385 PHE 0.019 0.002 PHE C 392 TYR 0.009 0.001 TYR A 367 ARG 0.004 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 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.673 Fit side-chains REVERT: A 115 TYR cc_start: 0.2445 (OUTLIER) cc_final: 0.2037 (t80) REVERT: A 385 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.6892 (p-80) REVERT: A 438 SER cc_start: 0.8212 (m) cc_final: 0.7889 (p) REVERT: B 105 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: B 361 GLN cc_start: 0.7587 (mt0) cc_final: 0.7272 (mm-40) REVERT: B 445 MET cc_start: 0.8433 (ttt) cc_final: 0.8224 (ttt) REVERT: B 482 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6845 (p90) REVERT: B 489 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8073 (m170) REVERT: C 103 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6452 (tm-30) outliers start: 22 outliers final: 16 residues processed: 98 average time/residue: 0.1401 time to fit residues: 19.5240 Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 480 ILE Chi-restraints excluded: chain B residue 102 LEU 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 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147758 restraints weight = 9582.969| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.38 r_work: 0.3516 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6144 Z= 0.200 Angle : 0.546 8.082 8343 Z= 0.288 Chirality : 0.041 0.139 930 Planarity : 0.003 0.036 1107 Dihedral : 4.207 20.682 870 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.32 % Allowed : 15.86 % Favored : 79.82 % 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: 1.19 (0.31), residues: 798 helix: 2.46 (0.25), residues: 431 sheet: 0.46 (0.47), residues: 130 loop : -2.35 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.011 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 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.631 Fit side-chains REVERT: A 115 TYR cc_start: 0.2252 (OUTLIER) cc_final: 0.2000 (t80) REVERT: A 385 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6760 (p-80) REVERT: A 438 SER cc_start: 0.8127 (m) cc_final: 0.7762 (p) REVERT: B 105 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: B 482 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6791 (p90) REVERT: B 489 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8202 (m170) REVERT: C 103 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6323 (tm-30) outliers start: 24 outliers final: 15 residues processed: 103 average time/residue: 0.1343 time to fit residues: 19.7303 Evaluate side-chains 100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 61 optimal weight: 0.0870 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.173270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147815 restraints weight = 9622.684| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.18 r_work: 0.3525 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6144 Z= 0.194 Angle : 0.546 8.161 8343 Z= 0.287 Chirality : 0.041 0.141 930 Planarity : 0.003 0.036 1107 Dihedral : 4.202 20.563 870 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.96 % Allowed : 16.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 798 helix: 2.47 (0.25), residues: 432 sheet: 0.70 (0.48), residues: 124 loop : -2.38 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 371 HIS 0.009 0.001 HIS B 385 PHE 0.018 0.002 PHE C 378 TYR 0.011 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 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.617 Fit side-chains REVERT: A 115 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.2276 (t80) REVERT: A 385 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7051 (p-80) REVERT: A 438 SER cc_start: 0.8190 (m) cc_final: 0.7843 (p) REVERT: B 105 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: B 482 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.6848 (p90) REVERT: B 489 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8259 (m170) REVERT: C 103 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6476 (tm-30) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.1353 time to fit residues: 18.5893 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.172236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146921 restraints weight = 9672.397| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.39 r_work: 0.3488 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6144 Z= 0.239 Angle : 0.565 7.998 8343 Z= 0.300 Chirality : 0.041 0.153 930 Planarity : 0.004 0.038 1107 Dihedral : 4.383 22.622 870 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.96 % Allowed : 15.86 % Favored : 80.18 % 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: 1.15 (0.31), residues: 798 helix: 2.36 (0.25), residues: 436 sheet: 0.27 (0.46), residues: 136 loop : -2.29 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.010 0.001 HIS B 385 PHE 0.018 0.002 PHE A 378 TYR 0.012 0.001 TYR A 367 ARG 0.004 0.000 ARG A 358 ********************** 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 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.614 Fit side-chains REVERT: A 115 TYR cc_start: 0.2696 (OUTLIER) cc_final: 0.2336 (t80) REVERT: A 385 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.6920 (p-80) REVERT: A 438 SER cc_start: 0.8185 (m) cc_final: 0.7842 (p) REVERT: B 92 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7849 (mt-10) REVERT: B 105 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: B 482 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7173 (p90) REVERT: B 489 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8324 (m170) REVERT: C 103 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6451 (tm-30) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.1438 time to fit residues: 21.4067 Evaluate side-chains 102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.172905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148830 restraints weight = 9713.193| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.91 r_work: 0.3514 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6144 Z= 0.274 Angle : 0.587 8.151 8343 Z= 0.313 Chirality : 0.042 0.162 930 Planarity : 0.004 0.037 1107 Dihedral : 4.574 24.311 870 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.78 % Allowed : 16.94 % 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: 1.06 (0.31), residues: 798 helix: 2.23 (0.25), residues: 436 sheet: 0.53 (0.48), residues: 125 loop : -2.29 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 371 HIS 0.011 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 A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.86 seconds wall clock time: 55 minutes 39.39 seconds (3339.39 seconds total)