Starting phenix.real_space_refine on Tue Jan 14 01:27:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef0_40857/01_2025/9ef0_40857.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 23 5.16 5 C 3147 2.51 5 N 858 2.21 5 O 962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4993 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4909 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 586} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'FAD': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.69, per 1000 atoms: 0.74 Number of scatterers: 4993 At special positions: 0 Unit cell: (69.876, 76.346, 87.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 3 15.00 O 962 8.00 N 858 7.00 C 3147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 585.3 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 41.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.092A pdb=" N ASP A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.096A pdb=" N ASP A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.536A pdb=" N LYS A 257 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 382 through 391 removed outlier: 4.574A pdb=" N GLN A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.587A pdb=" N GLU A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 536 through 553 removed outlier: 4.107A pdb=" N PHE A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 585 Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.590A pdb=" N LEU A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 removed outlier: 3.866A pdb=" N LYS A 618 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 624 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 655 through 669 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 112 removed outlier: 6.494A pdb=" N ILE A 80 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 112 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 82 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 133 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 171 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 135 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU A 173 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET A 137 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 168 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 112 removed outlier: 6.494A pdb=" N ILE A 80 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 112 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 82 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 133 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 171 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 135 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU A 173 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET A 137 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.634A pdb=" N ALA A 285 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 304 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A 289 " --> pdb=" O HIS A 302 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS A 302 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 291 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 300 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 479 Processing sheet with id=AA6, first strand: chain 'A' and resid 590 through 595 removed outlier: 6.838A pdb=" N THR A 560 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASN A 592 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 562 " --> pdb=" O ASN A 592 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA A 594 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR A 564 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 528 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR A 563 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET A 530 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY A 565 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 627 " --> pdb=" O SER A 673 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 549 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: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1033 1.33 - 1.45: 1260 1.45 - 1.57: 2780 1.57 - 1.69: 5 1.69 - 1.81: 39 Bond restraints: 5117 Sorted by residual: bond pdb=" CB ASP A 118 " pdb=" CG ASP A 118 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.51e-01 bond pdb=" CB MET A 541 " pdb=" CG MET A 541 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.46e-01 bond pdb=" C ILE A 377 " pdb=" O ILE A 377 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.47e-02 4.63e+03 6.19e-01 bond pdb=" CG PRO A 364 " pdb=" CD PRO A 364 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.70e-01 bond pdb=" CA ASP A 118 " pdb=" CB ASP A 118 " ideal model delta sigma weight residual 1.529 1.541 -0.012 1.61e-02 3.86e+03 5.57e-01 ... (remaining 5112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6851 1.92 - 3.84: 77 3.84 - 5.76: 11 5.76 - 7.68: 1 7.68 - 9.60: 2 Bond angle restraints: 6942 Sorted by residual: angle pdb=" N MET A 346 " pdb=" CA MET A 346 " pdb=" C MET A 346 " ideal model delta sigma weight residual 108.34 111.94 -3.60 1.31e+00 5.83e-01 7.56e+00 angle pdb=" CA LEU A 125 " pdb=" CB LEU A 125 " pdb=" CG LEU A 125 " ideal model delta sigma weight residual 116.30 125.90 -9.60 3.50e+00 8.16e-02 7.52e+00 angle pdb=" N VAL A 464 " pdb=" CA VAL A 464 " pdb=" C VAL A 464 " ideal model delta sigma weight residual 109.34 103.91 5.43 2.08e+00 2.31e-01 6.82e+00 angle pdb=" CB MET A 541 " pdb=" CG MET A 541 " pdb=" SD MET A 541 " ideal model delta sigma weight residual 112.70 104.97 7.73 3.00e+00 1.11e-01 6.64e+00 angle pdb=" C PHE A 181 " pdb=" CA PHE A 181 " pdb=" CB PHE A 181 " ideal model delta sigma weight residual 110.81 114.30 -3.49 1.65e+00 3.67e-01 4.48e+00 ... (remaining 6937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 2928 32.50 - 65.00: 121 65.00 - 97.49: 9 97.49 - 129.99: 0 129.99 - 162.49: 1 Dihedral angle restraints: 3059 sinusoidal: 1276 harmonic: 1783 Sorted by residual: dihedral pdb=" O5' FAD A 702 " pdb=" O3P FAD A 702 " pdb=" P FAD A 702 " pdb=" PA FAD A 702 " ideal model delta sinusoidal sigma weight residual -61.77 100.72 -162.49 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA PHE A 181 " pdb=" C PHE A 181 " pdb=" N ASN A 182 " pdb=" CA ASN A 182 " ideal model delta harmonic sigma weight residual -180.00 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CB GLU A 546 " pdb=" CG GLU A 546 " pdb=" CD GLU A 546 " pdb=" OE1 GLU A 546 " ideal model delta sinusoidal sigma weight residual 0.00 -84.24 84.24 1 3.00e+01 1.11e-03 9.60e+00 ... (remaining 3056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 445 0.031 - 0.061: 196 0.061 - 0.092: 53 0.092 - 0.123: 33 0.123 - 0.153: 1 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA VAL A 464 " pdb=" N VAL A 464 " pdb=" C VAL A 464 " pdb=" CB VAL A 464 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU A 351 " pdb=" CB LEU A 351 " pdb=" CD1 LEU A 351 " pdb=" CD2 LEU A 351 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA TRP A 224 " pdb=" N TRP A 224 " pdb=" C TRP A 224 " pdb=" CB TRP A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 725 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 652 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.24e+00 pdb=" N PRO A 653 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 653 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 653 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 465 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 466 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 532 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 533 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.018 5.00e-02 4.00e+02 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 393 2.74 - 3.28: 5041 3.28 - 3.82: 8498 3.82 - 4.36: 9841 4.36 - 4.90: 16898 Nonbonded interactions: 40671 Sorted by model distance: nonbonded pdb=" OG1 THR A 88 " pdb=" O1P FMN A 701 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 140 " pdb=" O2P FMN A 701 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP A 162 " pdb=" OG1 THR A 164 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASN A 96 " pdb=" OG SER A 111 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 117 " pdb=" OD1 ASN A 356 " model vdw 2.273 3.040 ... (remaining 40666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.890 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.002 0.024 5117 Z= 0.164 Angle : 0.542 9.600 6942 Z= 0.276 Chirality : 0.040 0.153 728 Planarity : 0.004 0.037 898 Dihedral : 16.797 162.487 1919 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.96 % Allowed : 22.75 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.33), residues: 611 helix: 0.64 (0.34), residues: 234 sheet: -0.70 (0.48), residues: 124 loop : -1.15 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 617 HIS 0.002 0.000 HIS A 319 PHE 0.010 0.001 PHE A 94 TYR 0.010 0.001 TYR A 455 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.613 Fit side-chains REVERT: A 257 LYS cc_start: 0.7716 (ptmt) cc_final: 0.7095 (tptp) REVERT: A 271 ASN cc_start: 0.7566 (p0) cc_final: 0.6636 (p0) REVERT: A 333 GLN cc_start: 0.7732 (mt0) cc_final: 0.7505 (tt0) REVERT: A 564 TYR cc_start: 0.7881 (t80) cc_final: 0.7544 (t80) REVERT: A 568 ARG cc_start: 0.6692 (mtp85) cc_final: 0.6353 (mtt-85) REVERT: A 595 PHE cc_start: 0.7496 (m-10) cc_final: 0.7287 (m-10) REVERT: A 632 ASP cc_start: 0.6951 (p0) cc_final: 0.6621 (m-30) outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.1815 time to fit residues: 22.5436 Evaluate side-chains 82 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 605 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 182 ASN A 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117906 restraints weight = 6771.930| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.98 r_work: 0.3317 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5117 Z= 0.205 Angle : 0.564 7.234 6942 Z= 0.287 Chirality : 0.042 0.150 728 Planarity : 0.004 0.039 898 Dihedral : 8.660 172.100 736 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.40 % Allowed : 19.31 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.34), residues: 611 helix: 0.77 (0.34), residues: 236 sheet: -0.59 (0.49), residues: 120 loop : -1.14 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 617 HIS 0.003 0.001 HIS A 319 PHE 0.013 0.002 PHE A 181 TYR 0.019 0.002 TYR A 478 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8430 (tp40) cc_final: 0.8163 (mm-40) REVERT: A 247 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7393 (mt) REVERT: A 257 LYS cc_start: 0.7801 (ptmt) cc_final: 0.7122 (tptp) REVERT: A 271 ASN cc_start: 0.7476 (p0) cc_final: 0.6751 (p0) REVERT: A 376 ASP cc_start: 0.8573 (t0) cc_final: 0.8260 (t0) REVERT: A 506 ARG cc_start: 0.5829 (mtm-85) cc_final: 0.5066 (mmm160) REVERT: A 564 TYR cc_start: 0.8037 (t80) cc_final: 0.7708 (t80) REVERT: A 632 ASP cc_start: 0.6943 (p0) cc_final: 0.6613 (m-30) REVERT: A 664 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8662 (mmtt) outliers start: 23 outliers final: 10 residues processed: 97 average time/residue: 0.1822 time to fit residues: 23.0933 Evaluate side-chains 87 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN A 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112859 restraints weight = 6963.494| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.08 r_work: 0.3251 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5117 Z= 0.252 Angle : 0.564 7.230 6942 Z= 0.288 Chirality : 0.043 0.181 728 Planarity : 0.004 0.036 898 Dihedral : 9.003 179.516 735 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.63 % Allowed : 20.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.34), residues: 611 helix: 0.73 (0.34), residues: 236 sheet: -0.72 (0.49), residues: 120 loop : -1.13 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 219 HIS 0.005 0.001 HIS A 319 PHE 0.014 0.002 PHE A 518 TYR 0.013 0.001 TYR A 575 ARG 0.006 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 244 GLN cc_start: 0.8478 (tp40) cc_final: 0.8202 (mm-40) REVERT: A 247 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7403 (mt) REVERT: A 257 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7252 (tptp) REVERT: A 271 ASN cc_start: 0.7504 (p0) cc_final: 0.6819 (p0) REVERT: A 376 ASP cc_start: 0.8574 (t0) cc_final: 0.8220 (t0) REVERT: A 411 GLU cc_start: 0.8119 (pm20) cc_final: 0.7520 (mm-30) REVERT: A 422 GLU cc_start: 0.8222 (tp30) cc_final: 0.7990 (tp30) REVERT: A 506 ARG cc_start: 0.5854 (mtm-85) cc_final: 0.5134 (mmm160) REVERT: A 564 TYR cc_start: 0.8108 (t80) cc_final: 0.7688 (t80) REVERT: A 595 PHE cc_start: 0.7351 (m-10) cc_final: 0.7148 (m-10) REVERT: A 632 ASP cc_start: 0.7013 (p0) cc_final: 0.6673 (m-30) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.1634 time to fit residues: 20.7064 Evaluate side-chains 89 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.144745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113469 restraints weight = 7043.376| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.07 r_work: 0.3344 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5117 Z= 0.174 Angle : 0.527 6.576 6942 Z= 0.269 Chirality : 0.041 0.166 728 Planarity : 0.004 0.038 898 Dihedral : 8.840 177.122 735 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.02 % Allowed : 20.08 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.34), residues: 611 helix: 0.83 (0.34), residues: 237 sheet: -0.61 (0.51), residues: 113 loop : -1.14 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 617 HIS 0.003 0.000 HIS A 319 PHE 0.014 0.002 PHE A 201 TYR 0.015 0.001 TYR A 367 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7689 (p) REVERT: A 244 GLN cc_start: 0.8503 (tp40) cc_final: 0.8217 (mm-40) REVERT: A 247 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7396 (mt) REVERT: A 257 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7224 (tptp) REVERT: A 271 ASN cc_start: 0.7471 (p0) cc_final: 0.6815 (p0) REVERT: A 376 ASP cc_start: 0.8532 (t0) cc_final: 0.8212 (t0) REVERT: A 422 GLU cc_start: 0.8218 (tp30) cc_final: 0.8010 (tp30) REVERT: A 446 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: A 506 ARG cc_start: 0.5787 (mtm-85) cc_final: 0.5150 (mmm160) REVERT: A 564 TYR cc_start: 0.8099 (t80) cc_final: 0.7703 (t80) REVERT: A 632 ASP cc_start: 0.6941 (p0) cc_final: 0.6648 (m-30) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 0.1658 time to fit residues: 21.3855 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 29 optimal weight: 0.0270 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118627 restraints weight = 7037.330| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.16 r_work: 0.3345 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5117 Z= 0.138 Angle : 0.518 8.388 6942 Z= 0.259 Chirality : 0.040 0.161 728 Planarity : 0.004 0.038 898 Dihedral : 8.389 168.885 735 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.44 % Allowed : 20.65 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.34), residues: 611 helix: 0.93 (0.34), residues: 236 sheet: -0.49 (0.51), residues: 113 loop : -1.13 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 617 HIS 0.002 0.000 HIS A 302 PHE 0.011 0.001 PHE A 201 TYR 0.017 0.001 TYR A 178 ARG 0.003 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 244 GLN cc_start: 0.8449 (tp40) cc_final: 0.8160 (mm-40) REVERT: A 247 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7358 (mt) REVERT: A 257 LYS cc_start: 0.7787 (ptmt) cc_final: 0.7135 (tptp) REVERT: A 271 ASN cc_start: 0.7461 (p0) cc_final: 0.6807 (p0) REVERT: A 376 ASP cc_start: 0.8555 (t0) cc_final: 0.8212 (t0) REVERT: A 391 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: A 411 GLU cc_start: 0.8119 (pm20) cc_final: 0.7556 (mm-30) REVERT: A 422 GLU cc_start: 0.8260 (tp30) cc_final: 0.8058 (tp30) REVERT: A 446 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: A 506 ARG cc_start: 0.5689 (mtm-85) cc_final: 0.5018 (mmm160) REVERT: A 564 TYR cc_start: 0.8012 (t80) cc_final: 0.7456 (t80) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.1659 time to fit residues: 21.7751 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.3980 chunk 53 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113782 restraints weight = 6980.220| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.10 r_work: 0.3263 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5117 Z= 0.225 Angle : 0.565 10.563 6942 Z= 0.281 Chirality : 0.042 0.159 728 Planarity : 0.004 0.042 898 Dihedral : 8.774 176.795 734 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.21 % Allowed : 21.80 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 611 helix: 0.84 (0.34), residues: 237 sheet: -0.57 (0.50), residues: 113 loop : -1.06 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.013 0.002 PHE A 201 TYR 0.018 0.002 TYR A 187 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8499 (tp40) cc_final: 0.8195 (mm-40) REVERT: A 247 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7336 (mt) REVERT: A 257 LYS cc_start: 0.7854 (ptmt) cc_final: 0.7239 (tptt) REVERT: A 271 ASN cc_start: 0.7491 (p0) cc_final: 0.6835 (p0) REVERT: A 376 ASP cc_start: 0.8545 (t0) cc_final: 0.8204 (t0) REVERT: A 391 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: A 422 GLU cc_start: 0.8279 (tp30) cc_final: 0.8071 (tp30) REVERT: A 446 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: A 506 ARG cc_start: 0.5778 (mtm-85) cc_final: 0.5073 (mmm160) REVERT: A 564 TYR cc_start: 0.8058 (t80) cc_final: 0.7608 (t80) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 0.1720 time to fit residues: 21.8361 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116466 restraints weight = 6936.225| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.11 r_work: 0.3337 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5117 Z= 0.158 Angle : 0.528 9.803 6942 Z= 0.262 Chirality : 0.040 0.155 728 Planarity : 0.004 0.042 898 Dihedral : 8.618 173.250 734 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.06 % Allowed : 22.94 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.34), residues: 611 helix: 0.94 (0.34), residues: 234 sheet: -0.54 (0.50), residues: 113 loop : -1.08 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 617 HIS 0.003 0.000 HIS A 319 PHE 0.010 0.001 PHE A 201 TYR 0.017 0.001 TYR A 178 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8458 (tp40) cc_final: 0.8138 (mm-40) REVERT: A 247 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7442 (tt) REVERT: A 257 LYS cc_start: 0.7830 (ptmt) cc_final: 0.7209 (tptt) REVERT: A 271 ASN cc_start: 0.7472 (p0) cc_final: 0.6812 (p0) REVERT: A 376 ASP cc_start: 0.8569 (t0) cc_final: 0.8174 (t0) REVERT: A 391 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: A 411 GLU cc_start: 0.8137 (pm20) cc_final: 0.7595 (mm-30) REVERT: A 446 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 506 ARG cc_start: 0.5759 (mtm-85) cc_final: 0.5062 (mmm160) REVERT: A 564 TYR cc_start: 0.8014 (t80) cc_final: 0.7531 (t80) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.1641 time to fit residues: 20.1895 Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112589 restraints weight = 7030.590| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.12 r_work: 0.3280 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5117 Z= 0.209 Angle : 0.561 9.221 6942 Z= 0.280 Chirality : 0.041 0.156 728 Planarity : 0.004 0.040 898 Dihedral : 8.914 178.396 734 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.44 % Allowed : 23.33 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.33), residues: 611 helix: 0.81 (0.34), residues: 237 sheet: -0.54 (0.51), residues: 113 loop : -1.08 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.012 0.002 PHE A 518 TYR 0.022 0.001 TYR A 367 ARG 0.009 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8474 (tp40) cc_final: 0.8153 (mm-40) REVERT: A 247 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7498 (tt) REVERT: A 257 LYS cc_start: 0.7830 (ptmt) cc_final: 0.7452 (tptp) REVERT: A 271 ASN cc_start: 0.7480 (p0) cc_final: 0.6817 (p0) REVERT: A 376 ASP cc_start: 0.8548 (t0) cc_final: 0.8161 (t0) REVERT: A 391 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: A 446 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: A 506 ARG cc_start: 0.5789 (mtm-85) cc_final: 0.5077 (mmm160) REVERT: A 564 TYR cc_start: 0.8077 (t80) cc_final: 0.7635 (t80) outliers start: 18 outliers final: 13 residues processed: 89 average time/residue: 0.1560 time to fit residues: 18.5736 Evaluate side-chains 89 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113505 restraints weight = 6880.168| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.05 r_work: 0.3301 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5117 Z= 0.223 Angle : 0.571 9.156 6942 Z= 0.287 Chirality : 0.042 0.158 728 Planarity : 0.004 0.040 898 Dihedral : 8.926 177.779 734 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.63 % Allowed : 23.33 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 611 helix: 0.78 (0.34), residues: 237 sheet: -0.68 (0.50), residues: 113 loop : -1.09 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.012 0.002 PHE A 518 TYR 0.022 0.001 TYR A 367 ARG 0.008 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8487 (tp40) cc_final: 0.8175 (mm-40) REVERT: A 247 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7519 (tt) REVERT: A 257 LYS cc_start: 0.7832 (ptmt) cc_final: 0.7489 (tptp) REVERT: A 271 ASN cc_start: 0.7468 (p0) cc_final: 0.6821 (p0) REVERT: A 376 ASP cc_start: 0.8560 (t0) cc_final: 0.8164 (t0) REVERT: A 391 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: A 398 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: A 422 GLU cc_start: 0.8249 (tp30) cc_final: 0.8020 (tp30) REVERT: A 446 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: A 506 ARG cc_start: 0.5798 (mtm-85) cc_final: 0.5151 (mmm160) REVERT: A 564 TYR cc_start: 0.8037 (t80) cc_final: 0.7586 (t80) REVERT: A 595 PHE cc_start: 0.7451 (m-10) cc_final: 0.7248 (m-10) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 0.1544 time to fit residues: 18.3691 Evaluate side-chains 87 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113613 restraints weight = 6990.210| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.00 r_work: 0.3296 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5117 Z= 0.223 Angle : 0.585 11.317 6942 Z= 0.291 Chirality : 0.042 0.158 728 Planarity : 0.004 0.044 898 Dihedral : 8.854 175.238 734 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.06 % Allowed : 23.52 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.33), residues: 611 helix: 0.72 (0.34), residues: 237 sheet: -0.77 (0.50), residues: 113 loop : -1.06 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.012 0.002 PHE A 518 TYR 0.020 0.001 TYR A 367 ARG 0.008 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8492 (tp40) cc_final: 0.8189 (mm-40) REVERT: A 247 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 257 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7543 (tptp) REVERT: A 271 ASN cc_start: 0.7499 (p0) cc_final: 0.6853 (p0) REVERT: A 376 ASP cc_start: 0.8580 (t0) cc_final: 0.8187 (t0) REVERT: A 391 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6551 (pm20) REVERT: A 422 GLU cc_start: 0.8225 (tp30) cc_final: 0.8006 (tp30) REVERT: A 446 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 506 ARG cc_start: 0.5807 (mtm-85) cc_final: 0.5179 (mmm160) REVERT: A 564 TYR cc_start: 0.8054 (t80) cc_final: 0.7586 (t80) REVERT: A 595 PHE cc_start: 0.7337 (m-10) cc_final: 0.7130 (m-10) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.1547 time to fit residues: 19.1906 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 630 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116614 restraints weight = 6976.021| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.07 r_work: 0.3315 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5117 Z= 0.169 Angle : 0.564 11.323 6942 Z= 0.280 Chirality : 0.041 0.153 728 Planarity : 0.004 0.041 898 Dihedral : 8.730 179.347 734 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.06 % Allowed : 23.71 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.34), residues: 611 helix: 0.93 (0.34), residues: 234 sheet: -0.76 (0.50), residues: 113 loop : -1.01 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 617 HIS 0.003 0.000 HIS A 319 PHE 0.009 0.001 PHE A 201 TYR 0.013 0.001 TYR A 367 ARG 0.008 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3169.47 seconds wall clock time: 57 minutes 39.49 seconds (3459.49 seconds total)