Starting phenix.real_space_refine on Wed Sep 17 15:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckz_45656/09_2025/9ckz_45656.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.050 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 40 5.16 5 C 6256 2.51 5 N 1551 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9475 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4925 Classifications: {'peptide': 591} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 573} Chain breaks: 3 Chain: "B" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4550 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 531} Chain breaks: 3 Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9475 At special positions: 0 Unit cell: (133.12, 78.208, 115.648, 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 40 16.00 O 1628 8.00 N 1551 7.00 C 6256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 339.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Proline residue: A 13 - end of helix Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 43 through 99 Processing helix chain 'A' and resid 124 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.859A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.795A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.666A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.233A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 402 removed outlier: 4.034A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.372A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 4.137A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.195A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.539A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 581 removed outlier: 3.791A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix removed outlier: 3.900A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.603A pdb=" N LEU A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 43 through 99 Processing helix chain 'B' and resid 124 through 168 removed outlier: 3.542A pdb=" N LEU B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 208 removed outlier: 3.504A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 232 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.640A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.639A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.684A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.405A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.776A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.353A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.742A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 581 removed outlier: 3.669A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix removed outlier: 3.977A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2169 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: 1.43 Time building geometry restraints manager: 1.20 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: 2627 1.34 - 1.46: 1880 1.46 - 1.58: 5171 1.58 - 1.70: 2 1.70 - 1.82: 58 Bond restraints: 9738 Sorted by residual: bond pdb=" C ASN A 204 " pdb=" N GLU A 205 " ideal model delta sigma weight residual 1.333 1.551 -0.218 1.51e-02 4.39e+03 2.08e+02 bond pdb=" N ALA A 625 " pdb=" CA ALA A 625 " ideal model delta sigma weight residual 1.457 1.486 -0.030 6.40e-03 2.44e+04 2.18e+01 bond pdb=" CA THR B 583 " pdb=" C THR B 583 " ideal model delta sigma weight residual 1.524 1.605 -0.082 2.25e-02 1.98e+03 1.32e+01 bond pdb=" N VAL A 626 " pdb=" CA VAL A 626 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.04e-02 9.25e+03 1.28e+01 bond pdb=" N VAL A 631 " pdb=" CA VAL A 631 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.18e-02 7.18e+03 1.13e+01 ... (remaining 9733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 13137 4.45 - 8.90: 47 8.90 - 13.35: 3 13.35 - 17.81: 5 17.81 - 22.26: 2 Bond angle restraints: 13194 Sorted by residual: angle pdb=" CA ASN A 204 " pdb=" C ASN A 204 " pdb=" N GLU A 205 " ideal model delta sigma weight residual 118.43 98.88 19.55 1.33e+00 5.65e-01 2.16e+02 angle pdb=" C ASN A 204 " pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 121.41 99.15 22.26 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O GLU A 207 " pdb=" C GLU A 207 " pdb=" N ASP A 208 " ideal model delta sigma weight residual 122.19 138.39 -16.20 1.34e+00 5.57e-01 1.46e+02 angle pdb=" CA GLU A 207 " pdb=" C GLU A 207 " pdb=" N ASP A 208 " ideal model delta sigma weight residual 117.20 101.04 16.16 1.45e+00 4.76e-01 1.24e+02 angle pdb=" C GLU A 207 " pdb=" N ASP A 208 " pdb=" CA ASP A 208 " ideal model delta sigma weight residual 122.07 106.44 15.63 1.43e+00 4.89e-01 1.19e+02 ... (remaining 13189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4872 17.97 - 35.93: 600 35.93 - 53.90: 145 53.90 - 71.87: 27 71.87 - 89.83: 11 Dihedral angle restraints: 5655 sinusoidal: 2280 harmonic: 3375 Sorted by residual: dihedral pdb=" CA LYS A 442 " pdb=" C LYS A 442 " pdb=" N TYR A 443 " pdb=" CA TYR A 443 " ideal model delta harmonic sigma weight residual 0.00 -38.43 38.43 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" CD ARG A 627 " pdb=" NE ARG A 627 " pdb=" CZ ARG A 627 " pdb=" NH1 ARG A 627 " ideal model delta sinusoidal sigma weight residual 0.00 -53.23 53.23 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLU B 90 " pdb=" C GLU B 90 " pdb=" N LEU B 91 " pdb=" CA LEU B 91 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1082 0.046 - 0.092: 295 0.092 - 0.138: 52 0.138 - 0.184: 12 0.184 - 0.229: 6 Chirality restraints: 1447 Sorted by residual: chirality pdb=" CA VAL A 626 " pdb=" N VAL A 626 " pdb=" C VAL A 626 " pdb=" CB VAL A 626 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 515 " pdb=" CA ILE B 515 " pdb=" CG1 ILE B 515 " pdb=" CG2 ILE B 515 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PHE A 623 " pdb=" N PHE A 623 " pdb=" C PHE A 623 " pdb=" CB PHE A 623 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1444 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 627 " -0.881 9.50e-02 1.11e+02 3.95e-01 9.47e+01 pdb=" NE ARG A 627 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 627 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 627 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 627 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 204 " 0.032 2.00e-02 2.50e+03 7.64e-02 5.83e+01 pdb=" C ASN A 204 " -0.131 2.00e-02 2.50e+03 pdb=" O ASN A 204 " 0.059 2.00e-02 2.50e+03 pdb=" N GLU A 205 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 258 " 0.029 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C LYS A 258 " -0.101 2.00e-02 2.50e+03 pdb=" O LYS A 258 " 0.038 2.00e-02 2.50e+03 pdb=" N LEU A 259 " 0.034 2.00e-02 2.50e+03 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 124 2.67 - 3.23: 9340 3.23 - 3.79: 15450 3.79 - 4.34: 19256 4.34 - 4.90: 32413 Nonbonded interactions: 76583 Sorted by model distance: nonbonded pdb=" O ARG A 263 " pdb=" NH1 ARG A 263 " model vdw 2.116 3.120 nonbonded pdb=" O ARG A 263 " pdb=" CZ ARG A 263 " model vdw 2.194 3.270 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.225 3.040 nonbonded pdb=" NH1 ARG B 472 " pdb=" OE2 GLU B 622 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG B 548 " pdb=" OE2 GLU B 613 " model vdw 2.294 3.120 ... (remaining 76578 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 419 or resid 444 through 625)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.140 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 9738 Z= 0.331 Angle : 0.841 22.256 13194 Z= 0.526 Chirality : 0.045 0.229 1447 Planarity : 0.011 0.395 1636 Dihedral : 16.830 89.833 3465 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.55 % Favored : 95.09 % Rotamer: Outliers : 1.38 % Allowed : 17.28 % Favored : 81.34 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.25), residues: 1121 helix: 2.12 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 624 TYR 0.016 0.002 TYR B 496 PHE 0.026 0.002 PHE A 58 TRP 0.026 0.002 TRP B 573 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9738) covalent geometry : angle 0.84092 (13194) hydrogen bonds : bond 0.11957 ( 726) hydrogen bonds : angle 4.93562 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.1000 time to fit residues: 14.3018 Evaluate side-chains 90 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 300 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 163 HIS A 648 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN B 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.232115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.201170 restraints weight = 10379.858| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.48 r_work: 0.3616 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9738 Z= 0.149 Angle : 0.562 6.894 13194 Z= 0.298 Chirality : 0.039 0.194 1447 Planarity : 0.004 0.063 1636 Dihedral : 5.355 51.160 1261 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 2.47 % Allowed : 16.09 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.25), residues: 1121 helix: 2.41 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.40 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 627 TYR 0.018 0.002 TYR A 347 PHE 0.025 0.001 PHE A 185 TRP 0.018 0.001 TRP B 573 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9738) covalent geometry : angle 0.56187 (13194) hydrogen bonds : bond 0.04845 ( 726) hydrogen bonds : angle 3.85818 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7761 (ptm160) REVERT: A 394 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7384 (p90) outliers start: 25 outliers final: 12 residues processed: 109 average time/residue: 0.0815 time to fit residues: 13.0740 Evaluate side-chains 99 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.0270 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 40.0000 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 40.0000 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 163 HIS ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.231661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.179581 restraints weight = 10353.966| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.37 r_work: 0.3235 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9738 Z= 0.134 Angle : 0.514 6.689 13194 Z= 0.276 Chirality : 0.038 0.190 1447 Planarity : 0.004 0.061 1636 Dihedral : 4.650 49.191 1253 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 16.58 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.25), residues: 1121 helix: 2.59 (0.16), residues: 899 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.016 0.001 TYR A 367 PHE 0.022 0.001 PHE A 58 TRP 0.015 0.001 TRP A 573 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9738) covalent geometry : angle 0.51443 (13194) hydrogen bonds : bond 0.04561 ( 726) hydrogen bonds : angle 3.69853 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7758 (tptt) REVERT: A 176 ARG cc_start: 0.6947 (ptm-80) cc_final: 0.6509 (ptm-80) REVERT: A 181 GLU cc_start: 0.7300 (pt0) cc_final: 0.6883 (tp30) REVERT: A 394 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 526 LEU cc_start: 0.8288 (tp) cc_final: 0.8087 (mt) outliers start: 24 outliers final: 10 residues processed: 104 average time/residue: 0.0838 time to fit residues: 13.0740 Evaluate side-chains 95 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** 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 = 0.4443 r_free = 0.4443 target = 0.227256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.197878 restraints weight = 10529.809| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.55 r_work: 0.3593 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9738 Z= 0.231 Angle : 0.622 9.099 13194 Z= 0.328 Chirality : 0.042 0.199 1447 Planarity : 0.005 0.065 1636 Dihedral : 4.821 54.661 1250 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 3.36 % Allowed : 17.08 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.25), residues: 1121 helix: 2.23 (0.16), residues: 903 sheet: None (None), residues: 0 loop : -1.63 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 270 TYR 0.025 0.002 TYR A 347 PHE 0.024 0.002 PHE B 185 TRP 0.021 0.002 TRP A 607 HIS 0.008 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 9738) covalent geometry : angle 0.62214 (13194) hydrogen bonds : bond 0.05714 ( 726) hydrogen bonds : angle 3.89706 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7065 (p90) outliers start: 34 outliers final: 17 residues processed: 116 average time/residue: 0.0903 time to fit residues: 15.2721 Evaluate side-chains 96 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.230834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.181176 restraints weight = 10541.486| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.08 r_work: 0.3199 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.003 0.053 9738 Z= 0.136 Angle : 0.527 8.447 13194 Z= 0.284 Chirality : 0.038 0.190 1447 Planarity : 0.004 0.063 1636 Dihedral : 4.628 50.860 1250 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.21 % Favored : 96.52 % Rotamer: Outliers : 3.46 % Allowed : 16.98 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.25), residues: 1121 helix: 2.52 (0.17), residues: 899 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.018 0.001 TYR A 367 PHE 0.023 0.001 PHE A 58 TRP 0.018 0.001 TRP B 573 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9738) covalent geometry : angle 0.52697 (13194) hydrogen bonds : bond 0.04714 ( 726) hydrogen bonds : angle 3.68120 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7566 (p90) REVERT: A 592 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7553 (tt) REVERT: B 394 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7204 (p90) REVERT: B 526 LEU cc_start: 0.8302 (mt) cc_final: 0.8084 (mt) REVERT: B 585 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6209 (tt) outliers start: 35 outliers final: 15 residues processed: 112 average time/residue: 0.0821 time to fit residues: 13.5663 Evaluate side-chains 99 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.233633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.193512 restraints weight = 10580.234| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.42 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 9738 Z= 0.254 Angle : 0.638 9.306 13194 Z= 0.338 Chirality : 0.043 0.204 1447 Planarity : 0.005 0.069 1636 Dihedral : 4.864 53.858 1250 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.90 % Rotamer: Outliers : 3.16 % Allowed : 18.26 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.25), residues: 1121 helix: 2.17 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -1.74 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.023 0.002 TYR A 347 PHE 0.024 0.002 PHE A 492 TRP 0.020 0.002 TRP A 607 HIS 0.007 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 9738) covalent geometry : angle 0.63827 (13194) hydrogen bonds : bond 0.05783 ( 726) hydrogen bonds : angle 3.88131 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 592 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 394 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6468 (p90) REVERT: B 577 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8159 (tt) outliers start: 32 outliers final: 19 residues processed: 110 average time/residue: 0.0785 time to fit residues: 13.0455 Evaluate side-chains 103 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 0.0070 chunk 71 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.237377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.197875 restraints weight = 10604.744| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.34 r_work: 0.3343 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9738 Z= 0.141 Angle : 0.536 8.295 13194 Z= 0.287 Chirality : 0.039 0.213 1447 Planarity : 0.004 0.066 1636 Dihedral : 4.657 49.974 1250 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 2.96 % Allowed : 18.07 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.25), residues: 1121 helix: 2.50 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.017 0.001 TYR A 367 PHE 0.026 0.001 PHE A 58 TRP 0.018 0.001 TRP B 266 HIS 0.005 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9738) covalent geometry : angle 0.53600 (13194) hydrogen bonds : bond 0.04719 ( 726) hydrogen bonds : angle 3.67367 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7479 (p90) REVERT: A 592 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7856 (tt) REVERT: B 394 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7081 (p90) outliers start: 30 outliers final: 14 residues processed: 108 average time/residue: 0.0758 time to fit residues: 12.4252 Evaluate side-chains 100 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.238269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200298 restraints weight = 10610.920| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.24 r_work: 0.3350 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9738 Z= 0.142 Angle : 0.561 8.401 13194 Z= 0.294 Chirality : 0.039 0.200 1447 Planarity : 0.004 0.065 1636 Dihedral : 4.574 47.775 1250 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.39 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 19.45 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.25), residues: 1121 helix: 2.57 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.015 0.001 TYR A 367 PHE 0.025 0.001 PHE A 58 TRP 0.017 0.001 TRP A 15 HIS 0.005 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9738) covalent geometry : angle 0.56058 (13194) hydrogen bonds : bond 0.04590 ( 726) hydrogen bonds : angle 3.62445 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7426 (p90) REVERT: A 592 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7828 (tt) REVERT: B 394 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7021 (p90) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.0872 time to fit residues: 13.3588 Evaluate side-chains 102 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 648 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 98 optimal weight: 0.0050 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.239560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.198045 restraints weight = 10611.488| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.41 r_work: 0.3310 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9738 Z= 0.125 Angle : 0.532 7.714 13194 Z= 0.283 Chirality : 0.038 0.195 1447 Planarity : 0.004 0.064 1636 Dihedral : 4.473 46.998 1250 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 2.17 % Allowed : 19.55 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.26), residues: 1121 helix: 2.68 (0.17), residues: 899 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.015 0.001 TYR B 518 PHE 0.023 0.001 PHE A 58 TRP 0.018 0.001 TRP B 266 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9738) covalent geometry : angle 0.53173 (13194) hydrogen bonds : bond 0.04238 ( 726) hydrogen bonds : angle 3.57084 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7505 (p90) REVERT: B 394 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7030 (p90) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.0853 time to fit residues: 13.8698 Evaluate side-chains 106 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 56 optimal weight: 0.0010 chunk 109 optimal weight: 0.0670 chunk 17 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.240671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.201747 restraints weight = 10524.949| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.21 r_work: 0.3690 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9738 Z= 0.120 Angle : 0.540 8.348 13194 Z= 0.284 Chirality : 0.038 0.229 1447 Planarity : 0.004 0.064 1636 Dihedral : 4.374 48.125 1250 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 2.17 % Allowed : 19.64 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.25), residues: 1121 helix: 2.78 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.015 0.001 TYR B 518 PHE 0.026 0.001 PHE A 58 TRP 0.018 0.001 TRP B 266 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9738) covalent geometry : angle 0.54011 (13194) hydrogen bonds : bond 0.04051 ( 726) hydrogen bonds : angle 3.52864 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7551 (p90) REVERT: A 410 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8461 (tt) REVERT: B 394 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6874 (p90) REVERT: B 401 ASN cc_start: 0.7821 (m-40) cc_final: 0.7594 (m-40) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.0881 time to fit residues: 14.0673 Evaluate side-chains 104 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 60 optimal weight: 40.0000 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.239299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198349 restraints weight = 10545.441| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.32 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9738 Z= 0.131 Angle : 0.547 8.432 13194 Z= 0.289 Chirality : 0.039 0.235 1447 Planarity : 0.004 0.065 1636 Dihedral : 3.959 23.663 1247 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 19.94 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.25), residues: 1121 helix: 2.78 (0.16), residues: 899 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.015 0.001 TYR B 518 PHE 0.015 0.001 PHE A 460 TRP 0.019 0.001 TRP B 573 HIS 0.006 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9738) covalent geometry : angle 0.54722 (13194) hydrogen bonds : bond 0.04199 ( 726) hydrogen bonds : angle 3.50647 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.22 seconds wall clock time: 35 minutes 0.84 seconds (2100.84 seconds total)