Starting phenix.real_space_refine on Wed Sep 17 05:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef0_40857/09_2025/9ef0_40857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef0_40857/09_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_40857/09_2025/9ef0_40857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef0_40857/09_2025/9ef0_40857.map" model { file = "/net/cci-nas-00/data/ceres_data/9ef0_40857/09_2025/9ef0_40857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef0_40857/09_2025/9ef0_40857.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.42, per 1000 atoms: 0.28 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: 0.42 Conformation dependent library (CDL) restraints added in 195.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 0.67 Time building geometry restraints manager: 0.55 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.030 ------------------------------------------------------------------------------- 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 : 10.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG A 454 TYR 0.010 0.001 TYR A 455 PHE 0.010 0.001 PHE A 94 TRP 0.011 0.001 TRP A 617 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5117) covalent geometry : angle 0.59153 ( 6942) hydrogen bonds : bond 0.16760 ( 189) hydrogen bonds : angle 6.92328 ( 549) *********************** 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 : 0.198 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: 0.0805 time to fit residues: 10.0593 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 : 0.157 ------------------------------------------------------------------------------- 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 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109822 restraints weight = 7043.963| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.09 r_work: 0.3236 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5117 Z= 0.237 Angle : 0.650 6.780 6942 Z= 0.333 Chirality : 0.045 0.160 728 Planarity : 0.005 0.038 899 Dihedral : 9.722 170.798 738 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.97 % Allowed : 20.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.33), residues: 611 helix: 0.51 (0.33), residues: 235 sheet: -0.78 (0.49), residues: 120 loop : -1.31 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 454 TYR 0.023 0.002 TYR A 478 PHE 0.019 0.002 PHE A 518 TRP 0.008 0.002 TRP A 219 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 5117) covalent geometry : angle 0.64987 ( 6942) hydrogen bonds : bond 0.03983 ( 189) hydrogen bonds : angle 5.12952 ( 549) *********************** 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 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 244 GLN cc_start: 0.8462 (tp40) cc_final: 0.8043 (mm-40) REVERT: A 247 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7631 (tt) REVERT: A 257 LYS cc_start: 0.8004 (ptmt) cc_final: 0.7374 (tptp) REVERT: A 271 ASN cc_start: 0.7540 (p0) cc_final: 0.6802 (p0) REVERT: A 411 GLU cc_start: 0.8085 (pm20) cc_final: 0.7504 (mm-30) REVERT: A 506 ARG cc_start: 0.5941 (mtm-85) cc_final: 0.5206 (mmm160) REVERT: A 564 TYR cc_start: 0.8152 (t80) cc_final: 0.7876 (t80) REVERT: A 632 ASP cc_start: 0.7051 (p0) cc_final: 0.6625 (m-30) REVERT: A 664 LYS cc_start: 0.8984 (mmtp) cc_final: 0.8678 (mmtt) outliers start: 26 outliers final: 13 residues processed: 102 average time/residue: 0.0719 time to fit residues: 9.5455 Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 486 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 576 ARG 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 51 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 642 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107973 restraints weight = 7125.705| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.07 r_work: 0.3199 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5117 Z= 0.215 Angle : 0.627 6.824 6942 Z= 0.321 Chirality : 0.045 0.160 728 Planarity : 0.004 0.039 899 Dihedral : 9.710 164.325 737 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.21 % Allowed : 22.94 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.33), residues: 611 helix: 0.51 (0.33), residues: 235 sheet: -0.89 (0.49), residues: 120 loop : -1.32 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 514 TYR 0.016 0.002 TYR A 575 PHE 0.017 0.002 PHE A 518 TRP 0.009 0.002 TRP A 617 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5117) covalent geometry : angle 0.62731 ( 6942) hydrogen bonds : bond 0.03808 ( 189) hydrogen bonds : angle 5.12206 ( 549) *********************** 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: 22 poor density : 83 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.8550 (tp40) cc_final: 0.8154 (mm-40) REVERT: A 247 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 257 LYS cc_start: 0.8009 (ptmt) cc_final: 0.7540 (tptp) REVERT: A 271 ASN cc_start: 0.7491 (p0) cc_final: 0.6807 (p0) REVERT: A 391 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6279 (pt0) REVERT: A 506 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5237 (mmm160) REVERT: A 564 TYR cc_start: 0.8125 (t80) cc_final: 0.7765 (t80) REVERT: A 568 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6377 (mtt-85) REVERT: A 632 ASP cc_start: 0.7068 (p0) cc_final: 0.6666 (m-30) outliers start: 22 outliers final: 16 residues processed: 101 average time/residue: 0.0788 time to fit residues: 10.2292 Evaluate side-chains 92 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 193 GLU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 391 GLN 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 576 ARG 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 650 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.3820 r_free = 0.3820 target = 0.142297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110857 restraints weight = 6944.834| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.04 r_work: 0.3248 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1878 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= 0.128 Angle : 0.554 7.351 6942 Z= 0.282 Chirality : 0.042 0.154 728 Planarity : 0.004 0.039 899 Dihedral : 9.613 169.222 737 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.59 % Allowed : 22.37 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.34), residues: 611 helix: 0.70 (0.34), residues: 236 sheet: -0.86 (0.49), residues: 120 loop : -1.21 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.014 0.001 TYR A 478 PHE 0.012 0.002 PHE A 518 TRP 0.007 0.001 TRP A 617 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5117) covalent geometry : angle 0.55433 ( 6942) hydrogen bonds : bond 0.03189 ( 189) hydrogen bonds : angle 4.77436 ( 549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8309 (m) cc_final: 0.7851 (p) REVERT: A 244 GLN cc_start: 0.8512 (tp40) cc_final: 0.8098 (mm-40) REVERT: A 247 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 257 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7364 (tptp) REVERT: A 271 ASN cc_start: 0.7512 (p0) cc_final: 0.6816 (p0) REVERT: A 376 ASP cc_start: 0.8553 (t0) cc_final: 0.8156 (t0) REVERT: A 398 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6346 (mt-10) REVERT: A 506 ARG cc_start: 0.5849 (mtm-85) cc_final: 0.5161 (mmm160) REVERT: A 564 TYR cc_start: 0.8115 (t80) cc_final: 0.7672 (t80) REVERT: A 568 ARG cc_start: 0.6634 (mtp85) cc_final: 0.6176 (mtt-85) REVERT: A 632 ASP cc_start: 0.6977 (p0) cc_final: 0.6627 (m-30) outliers start: 24 outliers final: 16 residues processed: 99 average time/residue: 0.0728 time to fit residues: 9.4204 Evaluate side-chains 95 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 162 ASP 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 365 THR Chi-restraints excluded: chain A residue 366 THR 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 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 576 ARG 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 2 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 44 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 182 ASN ** 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 = 0.3837 r_free = 0.3837 target = 0.143737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112181 restraints weight = 7092.145| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.04 r_work: 0.3259 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1951 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= 0.119 Angle : 0.541 7.820 6942 Z= 0.275 Chirality : 0.041 0.191 728 Planarity : 0.004 0.041 899 Dihedral : 9.556 171.861 737 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.59 % Allowed : 21.03 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.34), residues: 611 helix: 0.81 (0.34), residues: 236 sheet: -0.87 (0.50), residues: 120 loop : -1.12 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.015 0.001 TYR A 367 PHE 0.022 0.002 PHE A 201 TRP 0.007 0.001 TRP A 617 HIS 0.003 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5117) covalent geometry : angle 0.54125 ( 6942) hydrogen bonds : bond 0.02997 ( 189) hydrogen bonds : angle 4.59729 ( 549) *********************** 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 109 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8246 (m) cc_final: 0.7783 (p) REVERT: A 201 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 244 GLN cc_start: 0.8541 (tp40) cc_final: 0.8150 (mm-40) REVERT: A 247 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7374 (mt) REVERT: A 257 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7465 (tptp) REVERT: A 271 ASN cc_start: 0.7476 (p0) cc_final: 0.6799 (p0) REVERT: A 374 TYR cc_start: 0.8932 (m-80) cc_final: 0.8680 (m-10) REVERT: A 376 ASP cc_start: 0.8527 (t0) cc_final: 0.8125 (t0) REVERT: A 391 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: A 506 ARG cc_start: 0.5872 (mtm-85) cc_final: 0.5175 (mmm160) REVERT: A 564 TYR cc_start: 0.8129 (t80) cc_final: 0.7711 (t80) REVERT: A 568 ARG cc_start: 0.6688 (mtp85) cc_final: 0.6384 (mtt-85) REVERT: A 595 PHE cc_start: 0.7080 (m-10) cc_final: 0.6861 (m-10) REVERT: A 632 ASP cc_start: 0.6952 (p0) cc_final: 0.6652 (m-30) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 0.0749 time to fit residues: 9.9960 Evaluate side-chains 100 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 201 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 289 ASN 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 535 THR Chi-restraints excluded: chain A residue 576 ARG 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 13 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.5690 ------------------------------------------------------------------------------- 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 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN A 615 HIS A 642 ASN A 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.146644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114969 restraints weight = 7071.183| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.08 r_work: 0.3303 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5117 Z= 0.100 Angle : 0.520 8.287 6942 Z= 0.264 Chirality : 0.041 0.178 728 Planarity : 0.004 0.042 899 Dihedral : 9.568 178.288 737 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.74 % Allowed : 20.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.34), residues: 611 helix: 0.84 (0.34), residues: 236 sheet: -0.74 (0.49), residues: 118 loop : -1.11 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.012 0.001 TYR A 478 PHE 0.040 0.002 PHE A 181 TRP 0.008 0.001 TRP A 617 HIS 0.002 0.000 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 5117) covalent geometry : angle 0.51987 ( 6942) hydrogen bonds : bond 0.02794 ( 189) hydrogen bonds : angle 4.50264 ( 549) *********************** 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 118 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.8147 (m) cc_final: 0.7678 (p) REVERT: A 201 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6613 (t80) REVERT: A 242 ILE cc_start: 0.8983 (tp) cc_final: 0.8769 (tp) REVERT: A 244 GLN cc_start: 0.8589 (tp40) cc_final: 0.8218 (mm-40) REVERT: A 247 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7390 (mt) REVERT: A 257 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7240 (tptt) REVERT: A 271 ASN cc_start: 0.7455 (p0) cc_final: 0.6779 (p0) REVERT: A 376 ASP cc_start: 0.8524 (t0) cc_final: 0.8141 (t0) REVERT: A 391 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: A 506 ARG cc_start: 0.5791 (mtm-85) cc_final: 0.5089 (mmm160) REVERT: A 564 TYR cc_start: 0.8047 (t80) cc_final: 0.7628 (t80) REVERT: A 568 ARG cc_start: 0.6581 (mtp85) cc_final: 0.6189 (mtt-85) REVERT: A 632 ASP cc_start: 0.6891 (p0) cc_final: 0.6631 (m-30) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.0775 time to fit residues: 11.1366 Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 193 GLU Chi-restraints excluded: chain A residue 201 PHE 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 289 ASN Chi-restraints excluded: chain A residue 342 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 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 576 ARG 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 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 0.0970 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 182 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.146664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114768 restraints weight = 7004.953| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.08 r_work: 0.3276 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2246 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= 0.120 Angle : 0.542 7.333 6942 Z= 0.273 Chirality : 0.042 0.175 728 Planarity : 0.004 0.045 899 Dihedral : 9.570 177.694 737 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.78 % Allowed : 21.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.34), residues: 611 helix: 0.83 (0.34), residues: 236 sheet: -0.76 (0.50), residues: 118 loop : -1.05 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.012 0.001 TYR A 478 PHE 0.023 0.002 PHE A 181 TRP 0.007 0.001 TRP A 617 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5117) covalent geometry : angle 0.54202 ( 6942) hydrogen bonds : bond 0.02925 ( 189) hydrogen bonds : angle 4.50695 ( 549) *********************** 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 104 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ILE cc_start: 0.8984 (tp) cc_final: 0.8775 (tp) REVERT: A 244 GLN cc_start: 0.8629 (tp40) cc_final: 0.8378 (mm-40) REVERT: A 247 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7401 (mt) REVERT: A 257 LYS cc_start: 0.7858 (ptmt) cc_final: 0.7280 (tptt) REVERT: A 271 ASN cc_start: 0.7425 (p0) cc_final: 0.6763 (p0) REVERT: A 376 ASP cc_start: 0.8536 (t0) cc_final: 0.8170 (t0) REVERT: A 391 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6368 (pm20) REVERT: A 506 ARG cc_start: 0.5831 (mtm-85) cc_final: 0.5150 (mmm160) REVERT: A 564 TYR cc_start: 0.8043 (t80) cc_final: 0.7608 (t80) REVERT: A 568 ARG cc_start: 0.6488 (mtp85) cc_final: 0.6198 (mtt-85) REVERT: A 632 ASP cc_start: 0.6907 (p0) cc_final: 0.6655 (m-30) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.0733 time to fit residues: 9.4861 Evaluate side-chains 96 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 193 GLU 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 289 ASN Chi-restraints excluded: chain A residue 342 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 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 576 ARG 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 2 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 182 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105559 restraints weight = 7182.695| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.02 r_work: 0.3200 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5117 Z= 0.228 Angle : 0.636 7.733 6942 Z= 0.324 Chirality : 0.045 0.181 728 Planarity : 0.004 0.048 899 Dihedral : 9.733 160.732 737 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.16 % Allowed : 21.99 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.33), residues: 611 helix: 0.58 (0.34), residues: 236 sheet: -1.02 (0.48), residues: 125 loop : -1.17 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 514 TYR 0.015 0.002 TYR A 367 PHE 0.038 0.003 PHE A 201 TRP 0.010 0.002 TRP A 224 HIS 0.006 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 5117) covalent geometry : angle 0.63575 ( 6942) hydrogen bonds : bond 0.03693 ( 189) hydrogen bonds : angle 4.76453 ( 549) *********************** 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 106 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8235 (pm20) cc_final: 0.7994 (pm20) REVERT: A 247 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 257 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7634 (tptp) REVERT: A 271 ASN cc_start: 0.7466 (p0) cc_final: 0.6824 (p0) REVERT: A 376 ASP cc_start: 0.8515 (t0) cc_final: 0.8152 (t0) REVERT: A 391 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: A 398 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6401 (mt-10) REVERT: A 506 ARG cc_start: 0.5921 (mtm-85) cc_final: 0.5337 (mmm160) REVERT: A 564 TYR cc_start: 0.8174 (t80) cc_final: 0.7853 (t80) REVERT: A 568 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6246 (mtt-85) REVERT: A 632 ASP cc_start: 0.6944 (p0) cc_final: 0.6640 (m-30) outliers start: 27 outliers final: 17 residues processed: 101 average time/residue: 0.0789 time to fit residues: 10.2777 Evaluate side-chains 94 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 377 ILE Chi-restraints excluded: chain A residue 391 GLN Chi-restraints excluded: chain A residue 398 GLU 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 576 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 182 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.143821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111807 restraints weight = 7026.434| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.06 r_work: 0.3284 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2583 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= 0.126 Angle : 0.579 7.555 6942 Z= 0.291 Chirality : 0.043 0.260 728 Planarity : 0.004 0.046 899 Dihedral : 9.640 167.367 737 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.21 % Allowed : 23.52 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.34), residues: 611 helix: 0.65 (0.34), residues: 237 sheet: -1.03 (0.48), residues: 118 loop : -1.06 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.014 0.001 TYR A 478 PHE 0.021 0.002 PHE A 201 TRP 0.026 0.002 TRP A 617 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5117) covalent geometry : angle 0.57902 ( 6942) hydrogen bonds : bond 0.03062 ( 189) hydrogen bonds : angle 4.65749 ( 549) *********************** 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 : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8156 (pm20) cc_final: 0.7840 (pm20) REVERT: A 242 ILE cc_start: 0.9011 (tp) cc_final: 0.8800 (tp) REVERT: A 247 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7371 (mt) REVERT: A 257 LYS cc_start: 0.7896 (ptmt) cc_final: 0.7562 (tptp) REVERT: A 271 ASN cc_start: 0.7404 (p0) cc_final: 0.6741 (p0) REVERT: A 376 ASP cc_start: 0.8558 (t0) cc_final: 0.8138 (t0) REVERT: A 391 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: A 398 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6340 (mt-10) REVERT: A 506 ARG cc_start: 0.5880 (mtm-85) cc_final: 0.5258 (mmm160) REVERT: A 564 TYR cc_start: 0.8104 (t80) cc_final: 0.7674 (t80) REVERT: A 568 ARG cc_start: 0.6398 (mtp85) cc_final: 0.6128 (mtt-85) REVERT: A 632 ASP cc_start: 0.6897 (p0) cc_final: 0.6641 (m-30) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.0697 time to fit residues: 8.8223 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 : 0.189 ------------------------------------------------------------------------------- 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 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 528 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 576 ARG 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 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 182 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.145800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114116 restraints weight = 7055.297| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.07 r_work: 0.3296 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5117 Z= 0.120 Angle : 0.582 7.617 6942 Z= 0.293 Chirality : 0.043 0.269 728 Planarity : 0.004 0.048 899 Dihedral : 9.496 171.587 737 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.44 % Allowed : 24.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.34), residues: 611 helix: 0.78 (0.34), residues: 234 sheet: -1.04 (0.48), residues: 118 loop : -1.04 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 199 TYR 0.021 0.001 TYR A 374 PHE 0.024 0.002 PHE A 201 TRP 0.022 0.001 TRP A 617 HIS 0.003 0.001 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5117) covalent geometry : angle 0.58206 ( 6942) hydrogen bonds : bond 0.03025 ( 189) hydrogen bonds : angle 4.59427 ( 549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8138 (pm20) cc_final: 0.7917 (pm20) REVERT: A 242 ILE cc_start: 0.8992 (tp) cc_final: 0.8776 (tp) REVERT: A 247 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7360 (mt) REVERT: A 257 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7521 (tptp) REVERT: A 271 ASN cc_start: 0.7393 (p0) cc_final: 0.6717 (p0) REVERT: A 376 ASP cc_start: 0.8545 (t0) cc_final: 0.8102 (t0) REVERT: A 391 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: A 411 GLU cc_start: 0.8159 (pm20) cc_final: 0.7713 (mm-30) REVERT: A 506 ARG cc_start: 0.5856 (mtm-85) cc_final: 0.5217 (mmm160) REVERT: A 564 TYR cc_start: 0.8068 (t80) cc_final: 0.7671 (t80) REVERT: A 568 ARG cc_start: 0.6342 (mtp85) cc_final: 0.6089 (mtt-85) REVERT: A 595 PHE cc_start: 0.7111 (m-10) cc_final: 0.6903 (m-10) REVERT: A 632 ASP cc_start: 0.6862 (p0) cc_final: 0.6641 (m-30) outliers start: 18 outliers final: 16 residues processed: 92 average time/residue: 0.0763 time to fit residues: 9.2130 Evaluate side-chains 97 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 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 528 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 576 ARG 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 40 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.149125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117499 restraints weight = 7053.565| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.09 r_work: 0.3360 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2711 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= 0.101 Angle : 0.545 7.675 6942 Z= 0.276 Chirality : 0.041 0.211 728 Planarity : 0.004 0.045 899 Dihedral : 9.176 176.430 737 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.87 % Allowed : 24.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.34), residues: 611 helix: 0.93 (0.34), residues: 234 sheet: -0.94 (0.48), residues: 114 loop : -0.90 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.011 0.001 TYR A 374 PHE 0.012 0.001 PHE A 201 TRP 0.024 0.001 TRP A 617 HIS 0.003 0.000 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5117) covalent geometry : angle 0.54500 ( 6942) hydrogen bonds : bond 0.02765 ( 189) hydrogen bonds : angle 4.46353 ( 549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.46 seconds wall clock time: 29 minutes 32.67 seconds (1772.67 seconds total)