Starting phenix.real_space_refine on Sun Jul 27 14:57:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckz_45656/07_2025/9ckz_45656.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckz_45656/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ckz_45656/07_2025/9ckz_45656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckz_45656/07_2025/9ckz_45656.map" model { file = "/net/cci-nas-00/data/ceres_data/9ckz_45656/07_2025/9ckz_45656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckz_45656/07_2025/9ckz_45656.cif" } resolution = 3.45 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.85, per 1000 atoms: 0.62 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: 2.32 Conformation dependent library (CDL) restraints added in 982.5 milliseconds 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: 0.81 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: 2.45 Time building geometry restraints manager: 2.77 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.160 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- 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 : 8.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (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 TRP 0.026 0.002 TRP B 573 HIS 0.004 0.001 HIS A 504 PHE 0.026 0.002 PHE A 58 TYR 0.016 0.002 TYR B 496 ARG 0.006 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.11957 ( 726) hydrogen bonds : angle 4.93562 ( 2169) covalent geometry : bond 0.00535 ( 9738) covalent geometry : angle 0.84092 (13194) *********************** 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 : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.2251 time to fit residues: 32.2640 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 : 1.044 ------------------------------------------------------------------------------- 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 95 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 648 GLN 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 = 0.4347 r_free = 0.4347 target = 0.217510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178222 restraints weight = 10376.539| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.46 r_work: 0.3454 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9738 Z= 0.165 Angle : 0.578 6.926 13194 Z= 0.307 Chirality : 0.040 0.189 1447 Planarity : 0.004 0.063 1636 Dihedral : 5.405 52.269 1261 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.25), residues: 1121 helix: 2.32 (0.17), residues: 903 sheet: None (None), residues: 0 loop : -1.51 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 573 HIS 0.004 0.001 HIS B 313 PHE 0.025 0.001 PHE A 185 TYR 0.019 0.002 TYR A 347 ARG 0.005 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 726) hydrogen bonds : angle 3.90407 ( 2169) covalent geometry : bond 0.00374 ( 9738) covalent geometry : angle 0.57773 (13194) *********************** 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 115 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8236 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 176 ARG cc_start: 0.7963 (ptm-80) cc_final: 0.7576 (ptm160) REVERT: A 394 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7491 (p90) REVERT: A 592 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7689 (tt) outliers start: 25 outliers final: 11 residues processed: 109 average time/residue: 0.1933 time to fit residues: 30.8643 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 : 0.948 ------------------------------------------------------------------------------- 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 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 592 ILE 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 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 83 optimal weight: 0.0770 chunk 92 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.219442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183519 restraints weight = 10576.522| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.63 r_work: 0.3500 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9738 Z= 0.129 Angle : 0.509 6.779 13194 Z= 0.273 Chirality : 0.038 0.189 1447 Planarity : 0.004 0.061 1636 Dihedral : 4.666 49.329 1253 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 17.08 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.25), residues: 1121 helix: 2.62 (0.16), residues: 898 sheet: None (None), residues: 0 loop : -1.36 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 573 HIS 0.002 0.001 HIS B 313 PHE 0.021 0.001 PHE A 185 TYR 0.015 0.001 TYR A 367 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 726) hydrogen bonds : angle 3.70705 ( 2169) covalent geometry : bond 0.00280 ( 9738) covalent geometry : angle 0.50863 (13194) *********************** 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 112 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7491 (tptt) REVERT: A 394 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7441 (p90) REVERT: A 592 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 644 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6627 (tm-30) outliers start: 24 outliers final: 10 residues processed: 105 average time/residue: 0.1788 time to fit residues: 28.0384 Evaluate side-chains 97 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 A residue 592 ILE Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 334 CYS 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 27 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.230393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.178465 restraints weight = 10314.884| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.87 r_work: 0.3233 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9738 Z= 0.167 Angle : 0.549 6.953 13194 Z= 0.290 Chirality : 0.039 0.193 1447 Planarity : 0.004 0.062 1636 Dihedral : 4.560 50.633 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.30 % Favored : 96.43 % Rotamer: Outliers : 3.36 % Allowed : 16.78 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.25), residues: 1121 helix: 2.53 (0.16), residues: 904 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 573 HIS 0.005 0.001 HIS B 313 PHE 0.022 0.001 PHE A 58 TYR 0.018 0.002 TYR A 347 ARG 0.007 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 726) hydrogen bonds : angle 3.71201 ( 2169) covalent geometry : bond 0.00396 ( 9738) covalent geometry : angle 0.54875 (13194) *********************** 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 121 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7900 (tptt) REVERT: A 158 LYS cc_start: 0.8533 (mttm) cc_final: 0.8207 (mmtm) REVERT: A 270 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7506 (mtp85) REVERT: A 394 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7565 (p90) REVERT: A 592 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7583 (tt) REVERT: B 526 LEU cc_start: 0.8335 (mt) cc_final: 0.8039 (mt) outliers start: 34 outliers final: 16 residues processed: 115 average time/residue: 0.1865 time to fit residues: 31.7482 Evaluate side-chains 100 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 519 ILE Chi-restraints excluded: chain A residue 583 THR 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 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 65 optimal weight: 6.9990 chunk 63 optimal weight: 40.0000 chunk 47 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.230093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.180754 restraints weight = 10515.075| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.79 r_work: 0.3253 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9738 Z= 0.146 Angle : 0.530 8.634 13194 Z= 0.284 Chirality : 0.039 0.193 1447 Planarity : 0.004 0.060 1636 Dihedral : 4.543 50.006 1250 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.12 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 16.78 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.25), residues: 1121 helix: 2.60 (0.16), residues: 899 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.027 0.001 PHE B 156 TYR 0.017 0.002 TYR A 367 ARG 0.007 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 726) hydrogen bonds : angle 3.64354 ( 2169) covalent geometry : bond 0.00333 ( 9738) covalent geometry : angle 0.52970 (13194) *********************** 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 114 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.7864 (tptt) REVERT: A 158 LYS cc_start: 0.8569 (mttm) cc_final: 0.8260 (mmtm) REVERT: A 394 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 592 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7542 (tt) REVERT: B 526 LEU cc_start: 0.8298 (mt) cc_final: 0.7976 (mt) REVERT: B 585 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6083 (tt) outliers start: 32 outliers final: 15 residues processed: 110 average time/residue: 0.2710 time to fit residues: 44.0780 Evaluate side-chains 97 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 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 583 THR Chi-restraints excluded: chain A residue 592 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 334 CYS Chi-restraints excluded: chain B residue 342 ILE 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 26 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 18 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.228511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.177097 restraints weight = 10435.506| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.09 r_work: 0.3161 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9738 Z= 0.195 Angle : 0.578 8.656 13194 Z= 0.307 Chirality : 0.040 0.198 1447 Planarity : 0.004 0.062 1636 Dihedral : 4.663 52.097 1250 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 3.36 % Allowed : 17.47 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.25), residues: 1121 helix: 2.44 (0.16), residues: 905 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 607 HIS 0.006 0.001 HIS B 313 PHE 0.018 0.002 PHE B 185 TYR 0.021 0.002 TYR A 347 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 726) hydrogen bonds : angle 3.70735 ( 2169) covalent geometry : bond 0.00463 ( 9738) covalent geometry : angle 0.57847 (13194) *********************** 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 122 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6450 (pttp) REVERT: A 158 LYS cc_start: 0.8529 (mttm) cc_final: 0.8252 (mmtm) REVERT: A 585 LEU cc_start: 0.7768 (tp) cc_final: 0.7513 (tp) REVERT: A 592 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7822 (tt) REVERT: B 526 LEU cc_start: 0.8371 (mt) cc_final: 0.8076 (mt) REVERT: B 577 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7795 (tt) REVERT: B 585 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6260 (tt) outliers start: 34 outliers final: 20 residues processed: 117 average time/residue: 0.1861 time to fit residues: 32.0036 Evaluate side-chains 106 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 248 ASN 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 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 464 LEU 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 577 ILE Chi-restraints excluded: chain B residue 585 LEU 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 106 optimal weight: 0.0050 chunk 31 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.230899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.204371 restraints weight = 10457.672| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.39 r_work: 0.3605 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1905 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= 0.124 Angle : 0.513 7.537 13194 Z= 0.276 Chirality : 0.038 0.198 1447 Planarity : 0.004 0.059 1636 Dihedral : 4.500 48.697 1250 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.61 % Rotamer: Outliers : 2.76 % Allowed : 17.47 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1121 helix: 2.69 (0.16), residues: 898 sheet: None (None), residues: 0 loop : -1.47 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 573 HIS 0.014 0.001 HIS A 10 PHE 0.026 0.001 PHE A 58 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 726) hydrogen bonds : angle 3.56789 ( 2169) covalent geometry : bond 0.00260 ( 9738) covalent geometry : angle 0.51322 (13194) *********************** 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: 28 poor density : 87 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 592 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7442 (tt) REVERT: B 401 ASN cc_start: 0.7815 (m-40) cc_final: 0.7552 (m-40) REVERT: B 526 LEU cc_start: 0.8253 (mt) cc_final: 0.7947 (mt) REVERT: B 585 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6204 (tt) outliers start: 28 outliers final: 15 residues processed: 108 average time/residue: 0.1881 time to fit residues: 30.2378 Evaluate side-chains 102 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 248 ASN 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 512 TYR Chi-restraints excluded: chain A residue 592 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 342 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 585 LEU 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 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.220979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.193128 restraints weight = 10656.028| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.23 r_work: 0.3614 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9738 Z= 0.179 Angle : 0.577 8.611 13194 Z= 0.305 Chirality : 0.040 0.205 1447 Planarity : 0.004 0.061 1636 Dihedral : 4.575 49.545 1250 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 18.46 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.25), residues: 1121 helix: 2.51 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -1.55 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 573 HIS 0.005 0.001 HIS B 313 PHE 0.026 0.002 PHE A 58 TYR 0.018 0.002 TYR A 367 ARG 0.003 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 726) hydrogen bonds : angle 3.63173 ( 2169) covalent geometry : bond 0.00420 ( 9738) covalent geometry : angle 0.57738 (13194) *********************** 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 108 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8148 (t0) REVERT: A 592 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7733 (tt) REVERT: B 504 HIS cc_start: 0.3945 (t-90) cc_final: 0.3735 (m90) REVERT: B 526 LEU cc_start: 0.8408 (mt) cc_final: 0.8111 (mt) REVERT: B 585 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6552 (tt) outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 0.1874 time to fit residues: 28.4112 Evaluate side-chains 100 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 248 ASN 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 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 585 LEU 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 73 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.235831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196631 restraints weight = 10573.804| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.33 r_work: 0.3706 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9738 Z= 0.195 Angle : 0.588 7.561 13194 Z= 0.314 Chirality : 0.041 0.205 1447 Planarity : 0.004 0.061 1636 Dihedral : 4.669 50.869 1250 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.57 % Favored : 96.25 % Rotamer: Outliers : 2.57 % Allowed : 18.36 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1121 helix: 2.36 (0.17), residues: 906 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 607 HIS 0.005 0.001 HIS B 313 PHE 0.023 0.002 PHE A 58 TYR 0.019 0.002 TYR A 367 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 726) hydrogen bonds : angle 3.72712 ( 2169) covalent geometry : bond 0.00465 ( 9738) covalent geometry : angle 0.58769 (13194) *********************** 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 113 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 592 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7936 (tt) REVERT: B 526 LEU cc_start: 0.8428 (mt) cc_final: 0.8196 (mt) REVERT: B 585 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6477 (tt) outliers start: 26 outliers final: 17 residues processed: 106 average time/residue: 0.1883 time to fit residues: 29.5115 Evaluate side-chains 101 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 260 GLU 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 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 585 LEU 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 26 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.0970 chunk 81 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.238142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198446 restraints weight = 10666.522| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.36 r_work: 0.3648 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9738 Z= 0.141 Angle : 0.558 9.079 13194 Z= 0.295 Chirality : 0.039 0.203 1447 Planarity : 0.004 0.060 1636 Dihedral : 4.537 48.267 1250 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.21 % Favored : 96.61 % Rotamer: Outliers : 2.47 % Allowed : 18.46 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.25), residues: 1121 helix: 2.60 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -1.54 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 266 HIS 0.003 0.001 HIS A 616 PHE 0.027 0.001 PHE A 58 TYR 0.015 0.001 TYR A 367 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 726) hydrogen bonds : angle 3.60213 ( 2169) covalent geometry : bond 0.00319 ( 9738) covalent geometry : angle 0.55819 (13194) ********************** 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: 25 poor density : 86 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 394 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7549 (p90) REVERT: A 410 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 592 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 401 ASN cc_start: 0.7854 (m-40) cc_final: 0.7595 (m-40) REVERT: B 526 LEU cc_start: 0.8378 (mt) cc_final: 0.8093 (mt) REVERT: B 585 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6586 (tt) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.2159 time to fit residues: 34.8531 Evaluate side-chains 105 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 248 ASN 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 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 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 259 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 585 LEU 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 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.237842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.195286 restraints weight = 10586.445| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.41 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9738 Z= 0.146 Angle : 0.561 8.743 13194 Z= 0.297 Chirality : 0.039 0.203 1447 Planarity : 0.004 0.060 1636 Dihedral : 4.515 46.783 1250 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.57 % Favored : 96.25 % Rotamer: Outliers : 2.07 % Allowed : 18.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.25), residues: 1121 helix: 2.55 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 573 HIS 0.004 0.001 HIS B 313 PHE 0.024 0.001 PHE A 58 TYR 0.015 0.002 TYR A 367 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 726) hydrogen bonds : angle 3.61005 ( 2169) covalent geometry : bond 0.00332 ( 9738) covalent geometry : angle 0.56145 (13194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4777.95 seconds wall clock time: 86 minutes 4.18 seconds (5164.18 seconds total)