Starting phenix.real_space_refine on Sat May 10 03:52:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef0_40857/05_2025/9ef0_40857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef0_40857/05_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_40857/05_2025/9ef0_40857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef0_40857/05_2025/9ef0_40857.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef0_40857/05_2025/9ef0_40857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef0_40857/05_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-5687/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: 3.37, per 1000 atoms: 0.67 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: 1.15 Conformation dependent library (CDL) restraints added in 529.4 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: 0.54 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: 1.58 Time building geometry restraints manager: 1.36 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=" C4 FMN A 701 " pdb=" C4A FMN A 701 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4A FMN A 701 " pdb=" N5 FMN A 701 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O5' FMN A 701 " pdb=" P FMN A 701 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C10 FMN A 701 " pdb=" N1 FMN A 701 " ideal model delta sigma weight residual 1.317 1.381 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C10 FMN A 701 " pdb=" C4A FMN A 701 " ideal model delta sigma weight residual 1.443 1.388 0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 5112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6830 1.92 - 3.84: 90 3.84 - 5.76: 16 5.76 - 7.68: 4 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=" O3P FMN A 701 " pdb=" P FMN A 701 " pdb=" O5' FMN A 701 " ideal model delta sigma weight residual 102.33 109.54 -7.21 3.00e+00 1.11e-01 5.77e+00 ... (remaining 6937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 2927 32.50 - 65.00: 124 65.00 - 97.49: 9 97.49 - 129.99: 0 129.99 - 162.49: 1 Dihedral angle restraints: 3061 sinusoidal: 1278 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 3058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 442 0.031 - 0.061: 198 0.061 - 0.092: 54 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: 899 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 896 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- 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 : 0.004 0.099 5117 Z= 0.173 Angle : 0.592 9.600 6942 Z= 0.287 Chirality : 0.040 0.153 728 Planarity : 0.004 0.037 899 Dihedral : 16.915 162.487 1921 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 Details of bonding type rmsd hydrogen bonds : bond 0.16760 ( 189) hydrogen bonds : angle 6.92328 ( 549) covalent geometry : bond 0.00362 ( 5117) covalent geometry : angle 0.59153 ( 6942) *********************** 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 : 0.550 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: 0.1843 time to fit residues: 22.8003 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 : 0.610 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118501 restraints weight = 6756.791| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.98 r_work: 0.3322 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1163 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= 0.139 Angle : 0.563 7.327 6942 Z= 0.288 Chirality : 0.042 0.150 728 Planarity : 0.004 0.039 899 Dihedral : 9.213 171.573 738 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.02 % Allowed : 19.89 % Favored : 76.10 % 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: 0.78 (0.34), residues: 236 sheet: -0.58 (0.49), residues: 120 loop : -1.15 (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 0.012 0.002 PHE A 181 TYR 0.018 0.002 TYR A 478 ARG 0.005 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 189) hydrogen bonds : angle 5.09213 ( 549) covalent geometry : bond 0.00321 ( 5117) covalent geometry : angle 0.56272 ( 6942) *********************** 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 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 244 GLN cc_start: 0.8433 (tp40) cc_final: 0.8152 (mm-40) REVERT: A 247 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 257 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7120 (tptp) REVERT: A 271 ASN cc_start: 0.7485 (p0) cc_final: 0.6754 (p0) REVERT: A 376 ASP cc_start: 0.8568 (t0) cc_final: 0.8234 (t0) REVERT: A 506 ARG cc_start: 0.5831 (mtm-85) cc_final: 0.5073 (mmm160) REVERT: A 564 TYR cc_start: 0.8031 (t80) cc_final: 0.7698 (t80) REVERT: A 632 ASP cc_start: 0.6949 (p0) cc_final: 0.6614 (m-30) REVERT: A 664 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8663 (mmtt) outliers start: 21 outliers final: 9 residues processed: 95 average time/residue: 0.1743 time to fit residues: 21.4101 Evaluate side-chains 85 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.144534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112641 restraints weight = 6947.413| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.05 r_work: 0.3287 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5117 Z= 0.151 Angle : 0.552 7.089 6942 Z= 0.283 Chirality : 0.042 0.178 728 Planarity : 0.004 0.036 899 Dihedral : 9.458 177.789 737 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.63 % Allowed : 20.65 % Favored : 75.72 % 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 (0.34), residues: 611 helix: 0.77 (0.34), residues: 236 sheet: -0.71 (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 0.004 0.001 HIS A 319 PHE 0.013 0.002 PHE A 518 TYR 0.013 0.001 TYR A 478 ARG 0.007 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 189) hydrogen bonds : angle 4.79242 ( 549) covalent geometry : bond 0.00354 ( 5117) covalent geometry : angle 0.55239 ( 6942) *********************** 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 : 0.556 Fit side-chains revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 244 GLN cc_start: 0.8452 (tp40) cc_final: 0.8171 (mm-40) REVERT: A 247 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7390 (mt) REVERT: A 257 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7190 (tptp) REVERT: A 271 ASN cc_start: 0.7519 (p0) cc_final: 0.6826 (p0) REVERT: A 376 ASP cc_start: 0.8568 (t0) cc_final: 0.8196 (t0) REVERT: A 422 GLU cc_start: 0.8211 (tp30) cc_final: 0.7977 (tp30) REVERT: A 506 ARG cc_start: 0.5848 (mtm-85) cc_final: 0.5101 (mmm160) REVERT: A 564 TYR cc_start: 0.8082 (t80) cc_final: 0.7681 (t80) REVERT: A 595 PHE cc_start: 0.7311 (m-10) cc_final: 0.7095 (m-10) REVERT: A 632 ASP cc_start: 0.6957 (p0) cc_final: 0.6632 (m-30) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.1666 time to fit residues: 21.0211 Evaluate side-chains 87 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.147657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116259 restraints weight = 6969.110| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.08 r_work: 0.3310 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1594 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= 0.106 Angle : 0.521 6.635 6942 Z= 0.266 Chirality : 0.041 0.166 728 Planarity : 0.004 0.037 899 Dihedral : 9.255 174.111 737 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -0.41 (0.34), residues: 611 helix: 0.85 (0.34), residues: 237 sheet: -0.59 (0.51), residues: 113 loop : -1.12 (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 0.017 0.002 PHE A 201 TYR 0.015 0.001 TYR A 367 ARG 0.004 0.000 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 189) hydrogen bonds : angle 4.64229 ( 549) covalent geometry : bond 0.00242 ( 5117) covalent geometry : angle 0.52136 ( 6942) *********************** 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 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7714 (p) REVERT: A 244 GLN cc_start: 0.8474 (tp40) cc_final: 0.8159 (mm-40) REVERT: A 247 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7365 (mt) REVERT: A 257 LYS cc_start: 0.7824 (ptmt) cc_final: 0.7149 (tptp) REVERT: A 271 ASN cc_start: 0.7483 (p0) cc_final: 0.6823 (p0) REVERT: A 376 ASP cc_start: 0.8562 (t0) cc_final: 0.8237 (t0) REVERT: A 422 GLU cc_start: 0.8227 (tp30) cc_final: 0.8013 (tp30) REVERT: A 446 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: A 506 ARG cc_start: 0.5749 (mtm-85) cc_final: 0.5064 (mmm160) REVERT: A 564 TYR cc_start: 0.8037 (t80) cc_final: 0.7624 (t80) REVERT: A 632 ASP cc_start: 0.6930 (p0) cc_final: 0.6645 (m-30) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.1489 time to fit residues: 19.1132 Evaluate side-chains 96 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.0000 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.7566 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.146648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114845 restraints weight = 7100.765| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.14 r_work: 0.3310 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5117 Z= 0.106 Angle : 0.527 8.458 6942 Z= 0.263 Chirality : 0.041 0.161 728 Planarity : 0.004 0.039 899 Dihedral : 9.146 172.408 737 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -0.40 (0.34), residues: 611 helix: 0.89 (0.34), residues: 236 sheet: -0.56 (0.51), residues: 113 loop : -1.14 (0.36), residues: 262 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 0.012 0.002 PHE A 201 TYR 0.017 0.001 TYR A 187 ARG 0.006 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.02833 ( 189) hydrogen bonds : angle 4.58180 ( 549) covalent geometry : bond 0.00246 ( 5117) covalent geometry : angle 0.52654 ( 6942) *********************** 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 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7665 (p) REVERT: A 244 GLN cc_start: 0.8543 (tp40) cc_final: 0.8257 (mm-40) REVERT: A 247 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7376 (mt) REVERT: A 257 LYS cc_start: 0.7838 (ptmt) cc_final: 0.7170 (tptp) REVERT: A 271 ASN cc_start: 0.7502 (p0) cc_final: 0.6814 (p0) REVERT: A 376 ASP cc_start: 0.8539 (t0) cc_final: 0.8179 (t0) REVERT: A 391 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: A 422 GLU cc_start: 0.8271 (tp30) cc_final: 0.8069 (tp30) REVERT: A 446 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: A 506 ARG cc_start: 0.5743 (mtm-85) cc_final: 0.5040 (mmm160) REVERT: A 564 TYR cc_start: 0.8021 (t80) cc_final: 0.7552 (t80) REVERT: A 632 ASP cc_start: 0.6841 (p0) cc_final: 0.6599 (m-30) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.1935 time to fit residues: 26.4809 Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 144 ASP 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 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 603 VAL 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: 5.9990 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110403 restraints weight = 7027.679| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.07 r_work: 0.3216 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5117 Z= 0.208 Angle : 0.629 10.275 6942 Z= 0.314 Chirality : 0.044 0.171 728 Planarity : 0.004 0.045 899 Dihedral : 9.478 169.869 736 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.40 % Allowed : 21.03 % Favored : 74.57 % 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: -0.67 (0.33), residues: 611 helix: 0.62 (0.34), residues: 236 sheet: -0.90 (0.48), residues: 120 loop : -1.14 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 617 HIS 0.006 0.001 HIS A 319 PHE 0.017 0.002 PHE A 518 TYR 0.016 0.002 TYR A 373 ARG 0.008 0.001 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 189) hydrogen bonds : angle 4.78758 ( 549) covalent geometry : bond 0.00485 ( 5117) covalent geometry : angle 0.62885 ( 6942) *********************** 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 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7578 (tt) REVERT: A 257 LYS cc_start: 0.7950 (ptmt) cc_final: 0.7555 (tptp) REVERT: A 271 ASN cc_start: 0.7518 (p0) cc_final: 0.6853 (p0) REVERT: A 359 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.8003 (m90) REVERT: A 376 ASP cc_start: 0.8529 (t0) cc_final: 0.8159 (t0) REVERT: A 391 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6428 (pt0) REVERT: A 398 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: A 422 GLU cc_start: 0.8303 (tp30) cc_final: 0.8091 (tp30) REVERT: A 446 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: A 506 ARG cc_start: 0.5864 (mtm-85) cc_final: 0.5161 (mmm160) REVERT: A 564 TYR cc_start: 0.8130 (t80) cc_final: 0.7802 (t80) REVERT: A 632 ASP cc_start: 0.6928 (p0) cc_final: 0.6581 (m-30) outliers start: 23 outliers final: 13 residues processed: 101 average time/residue: 0.1409 time to fit residues: 19.0988 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 : 0.542 ------------------------------------------------------------------------------- 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 289 ASN Chi-restraints excluded: chain A residue 359 HIS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 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 603 VAL 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: 6.9990 chunk 41 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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** A 615 HIS A 642 ASN A 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113313 restraints weight = 6946.970| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.04 r_work: 0.3285 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5117 Z= 0.110 Angle : 0.555 10.008 6942 Z= 0.274 Chirality : 0.041 0.158 728 Planarity : 0.004 0.043 899 Dihedral : 9.497 176.554 736 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.82 % Allowed : 22.18 % 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: -0.52 (0.34), residues: 611 helix: 0.77 (0.34), residues: 236 sheet: -0.85 (0.49), residues: 118 loop : -1.07 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.009 0.001 PHE A 201 TYR 0.014 0.001 TYR A 367 ARG 0.006 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 189) hydrogen bonds : angle 4.63033 ( 549) covalent geometry : bond 0.00258 ( 5117) covalent geometry : angle 0.55463 ( 6942) *********************** 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 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7161 (tpp) cc_final: 0.6895 (tpp) REVERT: A 244 GLN cc_start: 0.8641 (tp40) cc_final: 0.8342 (mm-40) REVERT: A 247 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7490 (tt) REVERT: A 257 LYS cc_start: 0.7886 (ptmt) cc_final: 0.7299 (tptt) REVERT: A 271 ASN cc_start: 0.7459 (p0) cc_final: 0.6799 (p0) REVERT: A 374 TYR cc_start: 0.8893 (m-80) cc_final: 0.8675 (m-80) REVERT: A 376 ASP cc_start: 0.8539 (t0) cc_final: 0.8148 (t0) REVERT: A 391 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6455 (pm20) REVERT: A 398 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6275 (mt-10) REVERT: A 506 ARG cc_start: 0.5828 (mtm-85) cc_final: 0.5141 (mmm160) REVERT: A 564 TYR cc_start: 0.8028 (t80) cc_final: 0.7626 (t80) REVERT: A 632 ASP cc_start: 0.6894 (p0) cc_final: 0.6618 (m-30) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.1520 time to fit residues: 19.3518 Evaluate side-chains 96 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 162 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** A 642 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112362 restraints weight = 7035.209| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.09 r_work: 0.3281 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5117 Z= 0.116 Angle : 0.556 9.694 6942 Z= 0.276 Chirality : 0.041 0.158 728 Planarity : 0.004 0.043 899 Dihedral : 9.495 178.240 736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.02 % Allowed : 22.18 % Favored : 73.80 % 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: -0.50 (0.34), residues: 611 helix: 0.79 (0.34), residues: 236 sheet: -0.83 (0.49), residues: 118 loop : -1.07 (0.36), residues: 257 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 0.010 0.001 PHE A 518 TYR 0.016 0.001 TYR A 367 ARG 0.004 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.02891 ( 189) hydrogen bonds : angle 4.58708 ( 549) covalent geometry : bond 0.00273 ( 5117) covalent geometry : angle 0.55632 ( 6942) *********************** 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 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7210 (tpp) cc_final: 0.6860 (tpp) REVERT: A 242 ILE cc_start: 0.8989 (tp) cc_final: 0.8779 (tp) REVERT: A 247 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7295 (mt) REVERT: A 257 LYS cc_start: 0.7830 (ptmt) cc_final: 0.7275 (tptt) REVERT: A 271 ASN cc_start: 0.7437 (p0) cc_final: 0.6786 (p0) REVERT: A 376 ASP cc_start: 0.8533 (t0) cc_final: 0.8147 (t0) REVERT: A 391 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6482 (pm20) REVERT: A 506 ARG cc_start: 0.5820 (mtm-85) cc_final: 0.5160 (mmm160) REVERT: A 564 TYR cc_start: 0.8068 (t80) cc_final: 0.7702 (t80) REVERT: A 632 ASP cc_start: 0.6937 (p0) cc_final: 0.6676 (m-30) outliers start: 21 outliers final: 17 residues processed: 96 average time/residue: 0.1827 time to fit residues: 22.9965 Evaluate side-chains 95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 162 ASP 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 260 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR 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=1.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.142489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111041 restraints weight = 6944.157| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.03 r_work: 0.3261 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5117 Z= 0.142 Angle : 0.594 11.144 6942 Z= 0.295 Chirality : 0.042 0.181 728 Planarity : 0.004 0.044 899 Dihedral : 9.541 175.653 736 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.21 % Allowed : 21.99 % Favored : 73.80 % 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: -0.55 (0.34), residues: 611 helix: 0.74 (0.34), residues: 237 sheet: -1.01 (0.47), residues: 125 loop : -0.98 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.012 0.002 PHE A 518 TYR 0.031 0.001 TYR A 367 ARG 0.009 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 189) hydrogen bonds : angle 4.64798 ( 549) covalent geometry : bond 0.00333 ( 5117) covalent geometry : angle 0.59377 ( 6942) *********************** 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 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ILE cc_start: 0.8987 (tp) cc_final: 0.8771 (tp) REVERT: A 247 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7445 (tt) REVERT: A 257 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7491 (tptp) REVERT: A 271 ASN cc_start: 0.7445 (p0) cc_final: 0.6793 (p0) REVERT: A 376 ASP cc_start: 0.8531 (t0) cc_final: 0.8136 (t0) REVERT: A 391 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: A 422 GLU cc_start: 0.8269 (tp30) cc_final: 0.8040 (tp30) REVERT: A 446 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: A 506 ARG cc_start: 0.5832 (mtm-85) cc_final: 0.5199 (mmm160) REVERT: A 564 TYR cc_start: 0.8086 (t80) cc_final: 0.7690 (t80) REVERT: A 595 PHE cc_start: 0.7287 (m-10) cc_final: 0.7048 (m-10) REVERT: A 632 ASP cc_start: 0.6882 (p0) cc_final: 0.6637 (m-30) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.1613 time to fit residues: 21.1952 Evaluate side-chains 97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 162 ASP 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 260 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR 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 603 VAL 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 8.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.144230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112597 restraints weight = 7015.014| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.05 r_work: 0.3291 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2370 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= 0.136 Angle : 0.600 10.917 6942 Z= 0.298 Chirality : 0.042 0.166 728 Planarity : 0.004 0.045 899 Dihedral : 9.521 174.556 736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.82 % Allowed : 22.75 % 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: -0.56 (0.33), residues: 611 helix: 0.75 (0.34), residues: 235 sheet: -1.02 (0.48), residues: 118 loop : -1.02 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 617 HIS 0.004 0.001 HIS A 319 PHE 0.011 0.002 PHE A 518 TYR 0.017 0.001 TYR A 374 ARG 0.009 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 189) hydrogen bonds : angle 4.66850 ( 549) covalent geometry : bond 0.00320 ( 5117) covalent geometry : angle 0.59986 ( 6942) ********************** 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 103 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7145 (tpp) cc_final: 0.6831 (tpp) REVERT: A 242 ILE cc_start: 0.9004 (tp) cc_final: 0.8791 (tp) REVERT: A 247 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 257 LYS cc_start: 0.7837 (ptmt) cc_final: 0.7504 (tptp) REVERT: A 271 ASN cc_start: 0.7460 (p0) cc_final: 0.6818 (p0) REVERT: A 376 ASP cc_start: 0.8556 (t0) cc_final: 0.8149 (t0) REVERT: A 391 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: A 422 GLU cc_start: 0.8261 (tp30) cc_final: 0.8033 (tp30) REVERT: A 446 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: A 506 ARG cc_start: 0.5833 (mtm-85) cc_final: 0.5220 (mmm160) REVERT: A 564 TYR cc_start: 0.8115 (t80) cc_final: 0.7713 (t80) REVERT: A 595 PHE cc_start: 0.7308 (m-10) cc_final: 0.7050 (m-10) REVERT: A 632 ASP cc_start: 0.6890 (p0) cc_final: 0.6655 (m-30) outliers start: 20 outliers final: 17 residues processed: 97 average time/residue: 0.1908 time to fit residues: 24.1051 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 162 ASP 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 260 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR 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 603 VAL 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: 3.9990 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.0000 chunk 19 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.146394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114902 restraints weight = 7023.594| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.06 r_work: 0.3358 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5117 Z= 0.106 Angle : 0.577 11.454 6942 Z= 0.285 Chirality : 0.041 0.155 728 Planarity : 0.004 0.045 899 Dihedral : 9.424 178.905 736 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.44 % Allowed : 22.94 % Favored : 73.61 % 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: 0.90 (0.34), residues: 234 sheet: -0.98 (0.48), residues: 118 loop : -0.99 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 617 HIS 0.003 0.000 HIS A 302 PHE 0.008 0.001 PHE A 181 TYR 0.023 0.001 TYR A 367 ARG 0.008 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.02752 ( 189) hydrogen bonds : angle 4.61867 ( 549) covalent geometry : bond 0.00243 ( 5117) covalent geometry : angle 0.57686 ( 6942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.39 seconds wall clock time: 58 minutes 9.94 seconds (3489.94 seconds total)