Starting phenix.real_space_refine on Thu Mar 6 04:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef0_40857/03_2025/9ef0_40857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef0_40857/03_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_40857/03_2025/9ef0_40857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef0_40857/03_2025/9ef0_40857.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef0_40857/03_2025/9ef0_40857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef0_40857/03_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-5624/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: 4.09, per 1000 atoms: 0.82 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: 1.95 Conformation dependent library (CDL) restraints added in 478.2 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: 1.07 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: 2.56 Time building geometry restraints manager: 2.12 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 20.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- 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 : 0.554 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: 0.2218 time to fit residues: 27.8946 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 : 0.661 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118526 restraints weight = 6758.285| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.97 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: 0.7795 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 : 0.528 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8432 (tp40) cc_final: 0.8162 (mm-40) REVERT: A 247 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 257 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7121 (tptp) REVERT: A 271 ASN cc_start: 0.7484 (p0) cc_final: 0.6757 (p0) REVERT: A 376 ASP cc_start: 0.8575 (t0) cc_final: 0.8261 (t0) REVERT: A 506 ARG cc_start: 0.5827 (mtm-85) cc_final: 0.5064 (mmm160) REVERT: A 564 TYR cc_start: 0.8039 (t80) cc_final: 0.7710 (t80) REVERT: A 632 ASP cc_start: 0.6939 (p0) cc_final: 0.6609 (m-30) REVERT: A 664 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8661 (mmtt) outliers start: 23 outliers final: 10 residues processed: 97 average time/residue: 0.1908 time to fit residues: 24.0970 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 : 0.569 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.141219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108963 restraints weight = 7023.622| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.03 r_work: 0.3195 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5117 Z= 0.364 Angle : 0.639 7.904 6942 Z= 0.328 Chirality : 0.046 0.188 728 Planarity : 0.004 0.040 898 Dihedral : 9.169 166.230 735 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.63 % Allowed : 21.61 % Favored : 74.76 % 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: -0.79 (0.33), residues: 611 helix: 0.52 (0.33), residues: 235 sheet: -0.86 (0.49), residues: 120 loop : -1.27 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 219 HIS 0.007 0.001 HIS A 319 PHE 0.019 0.002 PHE A 518 TYR 0.017 0.002 TYR A 140 ARG 0.006 0.001 ARG A 454 *********************** 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 105 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8538 (tp40) cc_final: 0.8097 (mm-40) REVERT: A 247 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7625 (tt) REVERT: A 257 LYS cc_start: 0.8019 (ptmt) cc_final: 0.7527 (tptp) REVERT: A 271 ASN cc_start: 0.7530 (p0) cc_final: 0.6833 (p0) REVERT: A 422 GLU cc_start: 0.8267 (tp30) cc_final: 0.8048 (tp30) REVERT: A 506 ARG cc_start: 0.5924 (mtm-85) cc_final: 0.5193 (mmm160) REVERT: A 564 TYR cc_start: 0.8160 (t80) cc_final: 0.7833 (t80) REVERT: A 632 ASP cc_start: 0.7047 (p0) cc_final: 0.6657 (m-30) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 0.1568 time to fit residues: 21.0780 Evaluate side-chains 90 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113853 restraints weight = 6985.502| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.11 r_work: 0.3282 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1835 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= 0.180 Angle : 0.552 6.821 6942 Z= 0.280 Chirality : 0.042 0.172 728 Planarity : 0.004 0.039 898 Dihedral : 9.045 174.153 735 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.54 % Allowed : 20.27 % Favored : 74.19 % 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: -0.53 (0.34), residues: 611 helix: 0.81 (0.34), residues: 234 sheet: -0.68 (0.51), residues: 113 loop : -1.21 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.003 0.001 HIS A 319 PHE 0.020 0.002 PHE A 201 TYR 0.016 0.001 TYR A 575 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 112 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7771 (p) REVERT: A 244 GLN cc_start: 0.8521 (tp40) cc_final: 0.8220 (mm-40) REVERT: A 247 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7398 (mt) REVERT: A 257 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7311 (tptp) REVERT: A 271 ASN cc_start: 0.7463 (p0) cc_final: 0.6786 (p0) REVERT: A 376 ASP cc_start: 0.8573 (t0) cc_final: 0.8187 (t0) REVERT: A 391 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: A 398 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6405 (mt-10) REVERT: A 422 GLU cc_start: 0.8268 (tp30) cc_final: 0.8064 (tp30) REVERT: A 446 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: A 506 ARG cc_start: 0.5830 (mtm-85) cc_final: 0.5128 (mmm160) REVERT: A 564 TYR cc_start: 0.8114 (t80) cc_final: 0.7755 (t80) REVERT: A 632 ASP cc_start: 0.6944 (p0) cc_final: 0.6613 (m-30) outliers start: 29 outliers final: 15 residues processed: 104 average time/residue: 0.1509 time to fit residues: 21.0013 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU 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 Chi-restraints excluded: chain A residue 661 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 overall best weight: 1.0760 ------------------------------------------------------------------------------- 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 642 ASN 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 = 0.146017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114388 restraints weight = 7051.444| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.04 r_work: 0.3266 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1980 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= 0.192 Angle : 0.561 8.662 6942 Z= 0.281 Chirality : 0.042 0.167 728 Planarity : 0.004 0.041 898 Dihedral : 9.011 174.701 735 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.59 % Allowed : 20.65 % Favored : 74.76 % 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: 0.84 (0.34), residues: 236 sheet: -0.80 (0.49), residues: 120 loop : -1.14 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.004 0.000 HIS A 319 PHE 0.031 0.002 PHE A 201 TYR 0.018 0.001 TYR A 367 ARG 0.004 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 111 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7701 (p) REVERT: A 244 GLN cc_start: 0.8525 (tp40) cc_final: 0.8312 (mm-40) REVERT: A 247 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7386 (mt) REVERT: A 257 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7324 (tptp) REVERT: A 271 ASN cc_start: 0.7452 (p0) cc_final: 0.6797 (p0) REVERT: A 376 ASP cc_start: 0.8553 (t0) cc_final: 0.8187 (t0) REVERT: A 391 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: A 398 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: A 506 ARG cc_start: 0.5838 (mtm-85) cc_final: 0.5161 (mmm160) REVERT: A 564 TYR cc_start: 0.8104 (t80) cc_final: 0.7664 (t80) REVERT: A 632 ASP cc_start: 0.6953 (p0) cc_final: 0.6662 (m-30) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 0.1653 time to fit residues: 22.6060 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 228 CYS 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 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: 6.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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 = 0.3843 r_free = 0.3843 target = 0.144181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112093 restraints weight = 6974.087| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.06 r_work: 0.3245 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5117 Z= 0.217 Angle : 0.578 10.552 6942 Z= 0.288 Chirality : 0.042 0.164 728 Planarity : 0.004 0.044 898 Dihedral : 9.046 172.624 735 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.97 % Allowed : 21.22 % 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: -0.53 (0.34), residues: 611 helix: 0.82 (0.34), residues: 236 sheet: -0.78 (0.49), residues: 120 loop : -1.19 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 617 HIS 0.004 0.000 HIS A 319 PHE 0.028 0.002 PHE A 201 TYR 0.023 0.001 TYR A 367 ARG 0.005 0.000 ARG A 514 *********************** 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 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 164 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7693 (p) REVERT: A 184 MET cc_start: 0.7252 (tpp) cc_final: 0.6951 (tpp) REVERT: A 202 GLU cc_start: 0.8225 (pm20) cc_final: 0.7930 (pm20) REVERT: A 244 GLN cc_start: 0.8603 (tp40) cc_final: 0.8301 (mm-40) REVERT: A 247 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7383 (mt) REVERT: A 257 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7317 (tptt) REVERT: A 271 ASN cc_start: 0.7451 (p0) cc_final: 0.6796 (p0) REVERT: A 376 ASP cc_start: 0.8564 (t0) cc_final: 0.8189 (t0) REVERT: A 391 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: A 398 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: A 446 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: A 506 ARG cc_start: 0.5830 (mtm-85) cc_final: 0.5170 (mmm160) REVERT: A 564 TYR cc_start: 0.8090 (t80) cc_final: 0.7743 (t80) REVERT: A 595 PHE cc_start: 0.7103 (m-10) cc_final: 0.6886 (m-10) REVERT: A 632 ASP cc_start: 0.6950 (p0) cc_final: 0.6659 (m-30) outliers start: 26 outliers final: 17 residues processed: 99 average time/residue: 0.2169 time to fit residues: 28.9408 Evaluate side-chains 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 310 SER 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 403 HIS 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 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: 0.0980 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 642 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111986 restraints weight = 6942.151| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.04 r_work: 0.3230 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2306 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= 0.241 Angle : 0.584 9.716 6942 Z= 0.293 Chirality : 0.042 0.164 728 Planarity : 0.004 0.044 898 Dihedral : 9.092 169.138 735 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.16 % Allowed : 21.41 % 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: -0.57 (0.34), residues: 611 helix: 0.74 (0.34), residues: 237 sheet: -0.85 (0.49), residues: 120 loop : -1.14 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 617 HIS 0.005 0.001 HIS A 319 PHE 0.029 0.002 PHE A 201 TYR 0.014 0.001 TYR A 478 ARG 0.005 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 110 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7355 (tpp) cc_final: 0.7103 (tpp) REVERT: A 202 GLU cc_start: 0.8219 (pm20) cc_final: 0.7960 (pm20) REVERT: A 244 GLN cc_start: 0.8626 (tp40) cc_final: 0.8355 (mm-40) REVERT: A 247 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7382 (mt) REVERT: A 257 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7502 (tptp) REVERT: A 271 ASN cc_start: 0.7478 (p0) cc_final: 0.6806 (p0) REVERT: A 376 ASP cc_start: 0.8540 (t0) cc_final: 0.8145 (t0) REVERT: A 391 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6478 (pm20) REVERT: A 398 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: A 411 GLU cc_start: 0.8188 (pm20) cc_final: 0.7626 (mm-30) REVERT: A 422 GLU cc_start: 0.8248 (tp30) cc_final: 0.8002 (tp30) REVERT: A 506 ARG cc_start: 0.5848 (mtm-85) cc_final: 0.5220 (mmm160) REVERT: A 564 TYR cc_start: 0.8119 (t80) cc_final: 0.7762 (t80) REVERT: A 632 ASP cc_start: 0.6933 (p0) cc_final: 0.6641 (m-30) outliers start: 27 outliers final: 22 residues processed: 101 average time/residue: 0.1769 time to fit residues: 23.0665 Evaluate side-chains 102 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 228 CYS 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 403 HIS Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 441 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 A 642 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116936 restraints weight = 6957.758| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.07 r_work: 0.3321 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5117 Z= 0.153 Angle : 0.547 9.766 6942 Z= 0.273 Chirality : 0.041 0.157 728 Planarity : 0.004 0.044 898 Dihedral : 9.002 178.965 735 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.02 % Allowed : 23.52 % Favored : 72.47 % 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: -0.38 (0.34), residues: 611 helix: 0.90 (0.35), residues: 236 sheet: -0.65 (0.50), residues: 114 loop : -1.07 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 617 HIS 0.002 0.000 HIS A 302 PHE 0.020 0.001 PHE A 201 TYR 0.024 0.001 TYR A 367 ARG 0.006 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 108 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8170 (pm20) cc_final: 0.7879 (pm20) REVERT: A 242 ILE cc_start: 0.8997 (tp) cc_final: 0.8784 (tp) REVERT: A 244 GLN cc_start: 0.8649 (tp40) cc_final: 0.8390 (mm-40) REVERT: A 247 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7381 (mt) REVERT: A 257 LYS cc_start: 0.7820 (ptmt) cc_final: 0.7225 (tptt) REVERT: A 271 ASN cc_start: 0.7381 (p0) cc_final: 0.6740 (p0) REVERT: A 376 ASP cc_start: 0.8576 (t0) cc_final: 0.8173 (t0) REVERT: A 391 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: A 411 GLU cc_start: 0.8139 (pm20) cc_final: 0.7657 (mm-30) REVERT: A 422 GLU cc_start: 0.8220 (tp30) cc_final: 0.7993 (tp30) REVERT: A 506 ARG cc_start: 0.5811 (mtm-85) cc_final: 0.5207 (mmm160) REVERT: A 564 TYR cc_start: 0.8050 (t80) cc_final: 0.7638 (t80) REVERT: A 632 ASP cc_start: 0.6902 (p0) cc_final: 0.6679 (m-30) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.3964 time to fit residues: 52.9928 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 : 0.572 ------------------------------------------------------------------------------- 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 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 203 LEU 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 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108557 restraints weight = 6916.132| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.00 r_work: 0.3196 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5117 Z= 0.376 Angle : 0.671 8.041 6942 Z= 0.338 Chirality : 0.045 0.168 728 Planarity : 0.005 0.049 898 Dihedral : 9.181 161.522 735 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.02 % Allowed : 23.52 % Favored : 72.47 % 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: -0.76 (0.33), residues: 611 helix: 0.64 (0.34), residues: 236 sheet: -1.03 (0.48), residues: 120 loop : -1.25 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 219 HIS 0.007 0.001 HIS A 319 PHE 0.033 0.003 PHE A 201 TYR 0.024 0.002 TYR A 367 ARG 0.010 0.001 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 98 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8236 (pm20) cc_final: 0.7986 (pm20) REVERT: A 203 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 247 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7627 (tt) REVERT: A 257 LYS cc_start: 0.7945 (ptmt) cc_final: 0.7643 (tptp) REVERT: A 271 ASN cc_start: 0.7451 (p0) cc_final: 0.6809 (p0) REVERT: A 376 ASP cc_start: 0.8542 (t0) cc_final: 0.8132 (t0) REVERT: A 391 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: A 398 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: A 422 GLU cc_start: 0.8321 (tp30) cc_final: 0.8094 (tp30) REVERT: A 446 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: A 506 ARG cc_start: 0.5900 (mtm-85) cc_final: 0.5307 (mmm160) REVERT: A 564 TYR cc_start: 0.8192 (t80) cc_final: 0.7872 (t80) REVERT: A 632 ASP cc_start: 0.6947 (p0) cc_final: 0.6657 (m-30) outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 0.2723 time to fit residues: 32.2519 Evaluate side-chains 89 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 203 LEU 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 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: 0.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.145307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113436 restraints weight = 6983.994| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.07 r_work: 0.3301 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2580 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= 0.188 Angle : 0.584 8.593 6942 Z= 0.293 Chirality : 0.041 0.162 728 Planarity : 0.004 0.049 898 Dihedral : 8.951 169.188 735 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.63 % Allowed : 24.28 % Favored : 72.08 % 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: -0.59 (0.33), residues: 611 helix: 0.86 (0.34), residues: 234 sheet: -1.08 (0.48), residues: 118 loop : -1.15 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 617 HIS 0.003 0.001 HIS A 302 PHE 0.023 0.002 PHE A 201 TYR 0.018 0.001 TYR A 367 ARG 0.012 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 99 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8168 (pm20) cc_final: 0.7901 (pm20) REVERT: A 242 ILE cc_start: 0.9006 (tp) cc_final: 0.8791 (tp) REVERT: A 247 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7379 (mt) REVERT: A 257 LYS cc_start: 0.7876 (ptmt) cc_final: 0.7581 (tptp) REVERT: A 271 ASN cc_start: 0.7416 (p0) cc_final: 0.6772 (p0) REVERT: A 376 ASP cc_start: 0.8531 (t0) cc_final: 0.8098 (t0) REVERT: A 391 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: A 398 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: A 411 GLU cc_start: 0.8186 (pm20) cc_final: 0.7723 (mm-30) REVERT: A 422 GLU cc_start: 0.8270 (tp30) cc_final: 0.8056 (tp30) REVERT: A 564 TYR cc_start: 0.8134 (t80) cc_final: 0.7734 (t80) REVERT: A 568 ARG cc_start: 0.6501 (mtp85) cc_final: 0.6104 (mtt-85) REVERT: A 595 PHE cc_start: 0.7187 (m-10) cc_final: 0.6983 (m-10) REVERT: A 632 ASP cc_start: 0.6878 (p0) cc_final: 0.6637 (m-30) outliers start: 19 outliers final: 14 residues processed: 93 average time/residue: 0.3050 time to fit residues: 38.0953 Evaluate side-chains 93 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 162 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 260 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 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: 0.8980 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.146458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114737 restraints weight = 7021.905| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.07 r_work: 0.3307 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2636 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= 0.175 Angle : 0.576 8.457 6942 Z= 0.290 Chirality : 0.041 0.158 728 Planarity : 0.004 0.047 898 Dihedral : 8.830 174.216 735 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.06 % Allowed : 24.47 % Favored : 72.47 % 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: -0.49 (0.34), residues: 611 helix: 0.95 (0.35), residues: 234 sheet: -1.04 (0.48), residues: 118 loop : -1.09 (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 0.020 0.002 PHE A 201 TYR 0.016 0.001 TYR A 367 ARG 0.012 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3979.64 seconds wall clock time: 72 minutes 32.43 seconds (4352.43 seconds total)