Starting phenix.real_space_refine on Tue Feb 3 16:58:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1y_62758/02_2026/9l1y_62758.map" } resolution = 3.46 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= 0.002 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3452 2.51 5 N 878 2.21 5 O 911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5267 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5148 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {'CLR': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.33, per 1000 atoms: 0.25 Number of scatterers: 5267 At special positions: 0 Unit cell: (103.4, 93.5, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 911 8.00 N 878 7.00 C 3452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 450 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 801 " - " ASN A 550 " " NAG A 802 " - " ASN A 427 " " NAG B 1 " - " ASN A 570 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 284.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 49.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.619A pdb=" N THR A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.571A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 117 through 132 Processing helix chain 'A' and resid 134 through 151 Proline residue: A 145 - end of helix removed outlier: 3.753A pdb=" N LEU A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.898A pdb=" N TRP A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 3.753A pdb=" N LEU A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.970A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 186' Processing helix chain 'A' and resid 197 through 226 removed outlier: 3.642A pdb=" N ALA A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 272 Processing helix chain 'A' and resid 275 through 290 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.698A pdb=" N MET A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.781A pdb=" N SER A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 removed outlier: 3.917A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.913A pdb=" N HIS A 381 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.554A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 removed outlier: 3.970A pdb=" N ASN A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.885A pdb=" N LYS A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 516 " --> pdb=" O TRP A 512 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 621 removed outlier: 3.835A pdb=" N LEU A 609 " --> pdb=" O ASN A 605 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 675 Processing helix chain 'A' and resid 676 through 705 removed outlier: 3.993A pdb=" N ARG A 680 " --> pdb=" O PRO A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.633A pdb=" N VAL A 471 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 532 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET A 600 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 553 " --> pdb=" O MET A 600 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 602 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 551 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 553 " --> pdb=" O MET A 579 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 579 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.638A pdb=" N VAL A 589 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 564 203 hydrogen bonds defined for protein. 576 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: 0.55 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 789 1.29 - 1.42: 1565 1.42 - 1.55: 3016 1.55 - 1.68: 12 1.68 - 1.81: 42 Bond restraints: 5424 Sorted by residual: bond pdb=" C PRO A 308 " pdb=" O PRO A 308 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.14e+01 bond pdb=" CA SER A 306 " pdb=" CB SER A 306 " ideal model delta sigma weight residual 1.534 1.454 0.080 1.71e-02 3.42e+03 2.20e+01 bond pdb=" CAI Y01 A 804 " pdb=" CAK Y01 A 804 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta sigma weight residual 1.469 1.415 0.053 1.28e-02 6.10e+03 1.74e+01 bond pdb=" CA SER A 307 " pdb=" CB SER A 307 " ideal model delta sigma weight residual 1.530 1.468 0.062 1.58e-02 4.01e+03 1.52e+01 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 7234 2.70 - 5.41: 118 5.41 - 8.11: 18 8.11 - 10.82: 3 10.82 - 13.52: 4 Bond angle restraints: 7377 Sorted by residual: angle pdb=" N LEU A 309 " pdb=" CA LEU A 309 " pdb=" C LEU A 309 " ideal model delta sigma weight residual 113.61 102.19 11.42 1.50e+00 4.44e-01 5.80e+01 angle pdb=" C THR A 527 " pdb=" CA THR A 527 " pdb=" CB THR A 527 " ideal model delta sigma weight residual 114.41 100.89 13.52 2.30e+00 1.89e-01 3.46e+01 angle pdb=" N PHE A 310 " pdb=" CA PHE A 310 " pdb=" C PHE A 310 " ideal model delta sigma weight residual 112.88 106.13 6.75 1.29e+00 6.01e-01 2.74e+01 angle pdb=" N SER A 306 " pdb=" CA SER A 306 " pdb=" C SER A 306 " ideal model delta sigma weight residual 113.38 107.22 6.16 1.23e+00 6.61e-01 2.51e+01 angle pdb=" N ALA A 305 " pdb=" CA ALA A 305 " pdb=" C ALA A 305 " ideal model delta sigma weight residual 113.61 106.31 7.30 1.50e+00 4.44e-01 2.37e+01 ... (remaining 7372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2744 17.14 - 34.29: 403 34.29 - 51.43: 143 51.43 - 68.57: 26 68.57 - 85.72: 9 Dihedral angle restraints: 3325 sinusoidal: 1493 harmonic: 1832 Sorted by residual: dihedral pdb=" C THR A 527 " pdb=" N THR A 527 " pdb=" CA THR A 527 " pdb=" CB THR A 527 " ideal model delta harmonic sigma weight residual -122.00 -111.22 -10.78 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" C THR A 675 " pdb=" N THR A 675 " pdb=" CA THR A 675 " pdb=" CB THR A 675 " ideal model delta harmonic sigma weight residual -122.00 -131.47 9.47 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" CA ASN A 474 " pdb=" C ASN A 474 " pdb=" N ASP A 475 " pdb=" CA ASP A 475 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 716 0.073 - 0.147: 78 0.147 - 0.220: 6 0.220 - 0.293: 7 0.293 - 0.366: 2 Chirality restraints: 809 Sorted by residual: chirality pdb=" C17 CLR A 803 " pdb=" C13 CLR A 803 " pdb=" C16 CLR A 803 " pdb=" C20 CLR A 803 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 527 " pdb=" N THR A 527 " pdb=" C THR A 527 " pdb=" CB THR A 527 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C13 CLR A 803 " pdb=" C12 CLR A 803 " pdb=" C14 CLR A 803 " pdb=" C17 CLR A 803 " both_signs ideal model delta sigma weight residual False -2.93 -3.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 806 not shown) Planarity restraints: 915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 524 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ASP A 524 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP A 524 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 525 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 483 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 484 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 484 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 484 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 304 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C LEU A 304 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 304 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 305 " -0.012 2.00e-02 2.50e+03 ... (remaining 912 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 867 2.76 - 3.30: 4848 3.30 - 3.83: 8347 3.83 - 4.37: 9152 4.37 - 4.90: 16051 Nonbonded interactions: 39265 Sorted by model distance: nonbonded pdb=" ND2 ASN A 389 " pdb=" O ASN A 392 " model vdw 2.227 3.120 nonbonded pdb=" O VAL A 320 " pdb=" NE2 GLN A 328 " model vdw 2.256 3.120 nonbonded pdb=" O LEU A 269 " pdb=" OG SER A 275 " model vdw 2.256 3.040 nonbonded pdb=" O SER A 695 " pdb=" OG1 THR A 699 " model vdw 2.268 3.040 nonbonded pdb=" O PRO A 428 " pdb=" O6 NAG A 802 " model vdw 2.277 3.040 ... (remaining 39260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 5429 Z= 0.285 Angle : 0.866 13.524 7391 Z= 0.460 Chirality : 0.054 0.366 809 Planarity : 0.005 0.049 912 Dihedral : 18.244 85.715 2144 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.77 % Favored : 91.26 % Rotamer: Outliers : 1.43 % Allowed : 31.79 % Favored : 66.79 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.43 (0.35), residues: 618 helix: 0.52 (0.32), residues: 278 sheet: -1.31 (0.67), residues: 71 loop : -2.48 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.013 0.001 TYR A 415 PHE 0.013 0.001 PHE A 477 TRP 0.015 0.001 TRP A 315 HIS 0.009 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 5424) covalent geometry : angle 0.86362 ( 7377) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.37062 ( 2) hydrogen bonds : bond 0.16982 ( 203) hydrogen bonds : angle 5.19698 ( 576) link_BETA1-4 : bond 0.00143 ( 1) link_BETA1-4 : angle 1.13737 ( 3) link_NAG-ASN : bond 0.00238 ( 3) link_NAG-ASN : angle 1.96988 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6991 (mt) REVERT: A 525 ASN cc_start: 0.5596 (OUTLIER) cc_final: 0.5002 (p0) outliers start: 8 outliers final: 2 residues processed: 67 average time/residue: 0.0832 time to fit residues: 7.1560 Evaluate side-chains 63 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 525 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 525 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.208969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165881 restraints weight = 6096.069| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.25 r_work: 0.3411 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5429 Z= 0.135 Angle : 0.616 7.334 7391 Z= 0.310 Chirality : 0.040 0.157 809 Planarity : 0.005 0.050 912 Dihedral : 7.284 58.284 924 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.28 % Favored : 92.23 % Rotamer: Outliers : 4.64 % Allowed : 27.86 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.14 (0.35), residues: 618 helix: 0.67 (0.32), residues: 278 sheet: -1.13 (0.68), residues: 71 loop : -2.23 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.008 0.001 TYR A 162 PHE 0.013 0.001 PHE A 477 TRP 0.013 0.001 TRP A 198 HIS 0.019 0.002 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5424) covalent geometry : angle 0.61239 ( 7377) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.36897 ( 2) hydrogen bonds : bond 0.04833 ( 203) hydrogen bonds : angle 4.19411 ( 576) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 1.31078 ( 3) link_NAG-ASN : bond 0.00248 ( 3) link_NAG-ASN : angle 1.88257 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 271 PHE cc_start: 0.7094 (t80) cc_final: 0.6835 (t80) REVERT: A 408 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.6230 (t70) REVERT: A 525 ASN cc_start: 0.5750 (OUTLIER) cc_final: 0.5250 (p0) REVERT: A 603 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.5527 (p90) outliers start: 26 outliers final: 12 residues processed: 83 average time/residue: 0.0751 time to fit residues: 8.1999 Evaluate side-chains 74 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 13 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** 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 = 0.4377 r_free = 0.4377 target = 0.212279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165217 restraints weight = 6018.543| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.16 r_work: 0.3448 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5429 Z= 0.106 Angle : 0.572 7.661 7391 Z= 0.281 Chirality : 0.038 0.154 809 Planarity : 0.004 0.043 912 Dihedral : 6.727 59.487 922 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.63 % Favored : 92.88 % Rotamer: Outliers : 4.82 % Allowed : 28.04 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.93 (0.35), residues: 618 helix: 0.88 (0.32), residues: 278 sheet: -1.43 (0.65), residues: 79 loop : -2.03 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.007 0.001 TYR A 322 PHE 0.012 0.001 PHE A 281 TRP 0.010 0.001 TRP A 315 HIS 0.011 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5424) covalent geometry : angle 0.56896 ( 7377) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.32298 ( 2) hydrogen bonds : bond 0.03903 ( 203) hydrogen bonds : angle 3.93333 ( 576) link_BETA1-4 : bond 0.00114 ( 1) link_BETA1-4 : angle 1.18987 ( 3) link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 1.60246 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6822 (mt) REVERT: A 307 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 462 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5602 (pm20) REVERT: A 501 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.6717 (p-90) REVERT: A 525 ASN cc_start: 0.5838 (OUTLIER) cc_final: 0.5269 (p0) REVERT: A 586 TYR cc_start: 0.6590 (m-10) cc_final: 0.6361 (m-80) REVERT: A 603 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5500 (p90) REVERT: A 683 ARG cc_start: 0.8424 (tmm160) cc_final: 0.8216 (tmm160) REVERT: A 724 ASN cc_start: 0.7891 (t0) cc_final: 0.7328 (m110) outliers start: 27 outliers final: 9 residues processed: 92 average time/residue: 0.0807 time to fit residues: 9.7043 Evaluate side-chains 76 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.0050 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.208592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161072 restraints weight = 5983.567| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.22 r_work: 0.3483 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5429 Z= 0.149 Angle : 0.604 7.540 7391 Z= 0.298 Chirality : 0.040 0.157 809 Planarity : 0.005 0.054 912 Dihedral : 6.903 58.084 922 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.44 % Favored : 92.39 % Rotamer: Outliers : 4.29 % Allowed : 28.93 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.97 (0.35), residues: 618 helix: 0.88 (0.32), residues: 277 sheet: -1.26 (0.67), residues: 72 loop : -2.16 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.010 0.001 TYR A 322 PHE 0.012 0.001 PHE A 212 TRP 0.012 0.001 TRP A 198 HIS 0.011 0.002 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5424) covalent geometry : angle 0.59987 ( 7377) SS BOND : bond 0.00344 ( 1) SS BOND : angle 0.32282 ( 2) hydrogen bonds : bond 0.04445 ( 203) hydrogen bonds : angle 3.97259 ( 576) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.19603 ( 3) link_NAG-ASN : bond 0.00154 ( 3) link_NAG-ASN : angle 1.91599 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: A 462 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5486 (pm20) REVERT: A 518 GLU cc_start: 0.8212 (tt0) cc_final: 0.7862 (tm-30) REVERT: A 525 ASN cc_start: 0.5934 (OUTLIER) cc_final: 0.5448 (p0) REVERT: A 603 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5470 (p90) REVERT: A 683 ARG cc_start: 0.8434 (tmm160) cc_final: 0.8193 (tmm160) REVERT: A 724 ASN cc_start: 0.8094 (t0) cc_final: 0.7568 (m-40) outliers start: 24 outliers final: 17 residues processed: 76 average time/residue: 0.0805 time to fit residues: 8.0215 Evaluate side-chains 78 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.0050 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 50 optimal weight: 0.9980 overall best weight: 0.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.213264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.163603 restraints weight = 6062.060| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.07 r_work: 0.3511 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5429 Z= 0.100 Angle : 0.555 7.638 7391 Z= 0.274 Chirality : 0.038 0.156 809 Planarity : 0.004 0.056 912 Dihedral : 6.654 59.746 922 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.47 % Favored : 93.37 % Rotamer: Outliers : 4.64 % Allowed : 28.75 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.74 (0.35), residues: 618 helix: 1.06 (0.32), residues: 277 sheet: -1.13 (0.67), residues: 72 loop : -2.02 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.009 0.001 TYR A 322 PHE 0.016 0.001 PHE A 281 TRP 0.011 0.001 TRP A 315 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 5424) covalent geometry : angle 0.55244 ( 7377) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.34456 ( 2) hydrogen bonds : bond 0.03634 ( 203) hydrogen bonds : angle 3.82955 ( 576) link_BETA1-4 : bond 0.00169 ( 1) link_BETA1-4 : angle 1.20759 ( 3) link_NAG-ASN : bond 0.00316 ( 3) link_NAG-ASN : angle 1.62224 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6775 (mt) REVERT: A 282 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6809 (t80) REVERT: A 462 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5474 (pm20) REVERT: A 501 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.6686 (p-90) REVERT: A 513 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5848 (mtt90) REVERT: A 518 GLU cc_start: 0.8281 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 525 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.5440 (p0) REVERT: A 603 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5555 (p90) REVERT: A 683 ARG cc_start: 0.8423 (tmm160) cc_final: 0.8174 (tmm160) REVERT: A 724 ASN cc_start: 0.8050 (t0) cc_final: 0.7550 (m-40) outliers start: 26 outliers final: 9 residues processed: 81 average time/residue: 0.0871 time to fit residues: 9.1063 Evaluate side-chains 77 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** 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 = 0.4318 r_free = 0.4318 target = 0.205728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159980 restraints weight = 6113.377| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.37 r_work: 0.3276 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5429 Z= 0.196 Angle : 0.645 8.819 7391 Z= 0.320 Chirality : 0.042 0.156 809 Planarity : 0.005 0.059 912 Dihedral : 7.041 58.482 922 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.61 % Favored : 92.23 % Rotamer: Outliers : 5.36 % Allowed : 29.29 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.04 (0.35), residues: 618 helix: 0.84 (0.32), residues: 277 sheet: -0.99 (0.68), residues: 64 loop : -2.28 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.011 0.001 TYR A 322 PHE 0.015 0.002 PHE A 212 TRP 0.014 0.002 TRP A 315 HIS 0.014 0.002 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5424) covalent geometry : angle 0.64047 ( 7377) SS BOND : bond 0.00389 ( 1) SS BOND : angle 0.43281 ( 2) hydrogen bonds : bond 0.05010 ( 203) hydrogen bonds : angle 4.09994 ( 576) link_BETA1-4 : bond 0.00146 ( 1) link_BETA1-4 : angle 1.29223 ( 3) link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 2.15476 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6800 (mt) REVERT: A 462 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5506 (pm20) REVERT: A 501 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.6653 (p-90) REVERT: A 513 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5645 (mtt90) REVERT: A 518 GLU cc_start: 0.8338 (tt0) cc_final: 0.8051 (tm-30) REVERT: A 525 ASN cc_start: 0.5901 (OUTLIER) cc_final: 0.5539 (p0) REVERT: A 603 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.5511 (p90) REVERT: A 683 ARG cc_start: 0.8432 (tmm160) cc_final: 0.8199 (tmm160) REVERT: A 724 ASN cc_start: 0.8229 (t0) cc_final: 0.7618 (m110) outliers start: 30 outliers final: 16 residues processed: 83 average time/residue: 0.0821 time to fit residues: 8.8932 Evaluate side-chains 79 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 52 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.211522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.158740 restraints weight = 6070.732| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.61 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5429 Z= 0.104 Angle : 0.570 6.747 7391 Z= 0.280 Chirality : 0.038 0.154 809 Planarity : 0.004 0.060 912 Dihedral : 6.682 59.186 922 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.63 % Favored : 93.20 % Rotamer: Outliers : 4.11 % Allowed : 30.71 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.83 (0.35), residues: 618 helix: 0.94 (0.32), residues: 284 sheet: -0.72 (0.70), residues: 64 loop : -2.22 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 TYR 0.009 0.001 TYR A 322 PHE 0.012 0.001 PHE A 281 TRP 0.013 0.001 TRP A 198 HIS 0.006 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5424) covalent geometry : angle 0.56702 ( 7377) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.39280 ( 2) hydrogen bonds : bond 0.03729 ( 203) hydrogen bonds : angle 3.82712 ( 576) link_BETA1-4 : bond 0.00139 ( 1) link_BETA1-4 : angle 1.23760 ( 3) link_NAG-ASN : bond 0.00289 ( 3) link_NAG-ASN : angle 1.66219 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5397 (ptt90) REVERT: A 264 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6773 (mt) REVERT: A 462 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5325 (pm20) REVERT: A 501 TRP cc_start: 0.7831 (OUTLIER) cc_final: 0.6844 (p-90) REVERT: A 513 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5721 (mtt90) REVERT: A 525 ASN cc_start: 0.5899 (OUTLIER) cc_final: 0.5552 (p0) REVERT: A 603 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.5349 (p90) REVERT: A 683 ARG cc_start: 0.8417 (tmm160) cc_final: 0.8176 (tmm160) outliers start: 23 outliers final: 11 residues processed: 77 average time/residue: 0.0937 time to fit residues: 9.1162 Evaluate side-chains 76 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.211048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.160289 restraints weight = 6007.358| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.85 r_work: 0.3348 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5429 Z= 0.116 Angle : 0.577 6.719 7391 Z= 0.282 Chirality : 0.039 0.153 809 Planarity : 0.004 0.061 912 Dihedral : 6.616 59.952 922 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.77 % Favored : 92.07 % Rotamer: Outliers : 3.93 % Allowed : 31.07 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.79 (0.35), residues: 618 helix: 0.91 (0.31), residues: 284 sheet: -0.68 (0.70), residues: 64 loop : -2.12 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.010 0.001 TYR A 322 PHE 0.011 0.001 PHE A 281 TRP 0.014 0.001 TRP A 315 HIS 0.008 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5424) covalent geometry : angle 0.57340 ( 7377) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.34339 ( 2) hydrogen bonds : bond 0.03826 ( 203) hydrogen bonds : angle 3.81154 ( 576) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 1.13829 ( 3) link_NAG-ASN : bond 0.00216 ( 3) link_NAG-ASN : angle 1.73274 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7942 (mtp180) REVERT: A 264 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6711 (mt) REVERT: A 462 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5322 (pm20) REVERT: A 501 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.6563 (p-90) REVERT: A 513 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.5653 (mtt90) REVERT: A 525 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.5616 (p0) REVERT: A 603 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5408 (p90) REVERT: A 683 ARG cc_start: 0.8379 (tmm160) cc_final: 0.8141 (tmm160) outliers start: 22 outliers final: 13 residues processed: 77 average time/residue: 0.0692 time to fit residues: 6.9628 Evaluate side-chains 79 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157801 restraints weight = 6015.582| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.00 r_work: 0.3338 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5429 Z= 0.132 Angle : 0.592 6.553 7391 Z= 0.291 Chirality : 0.039 0.154 809 Planarity : 0.004 0.064 912 Dihedral : 6.635 59.640 922 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.96 % Favored : 92.88 % Rotamer: Outliers : 4.11 % Allowed : 31.07 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.88 (0.35), residues: 618 helix: 0.80 (0.32), residues: 286 sheet: -0.73 (0.70), residues: 64 loop : -2.15 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.010 0.001 TYR A 322 PHE 0.011 0.001 PHE A 212 TRP 0.016 0.001 TRP A 315 HIS 0.010 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5424) covalent geometry : angle 0.58865 ( 7377) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.38995 ( 2) hydrogen bonds : bond 0.04053 ( 203) hydrogen bonds : angle 3.90107 ( 576) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.11786 ( 3) link_NAG-ASN : bond 0.00163 ( 3) link_NAG-ASN : angle 1.82480 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5349 (ptt90) REVERT: A 264 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6722 (mt) REVERT: A 462 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: A 501 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.6557 (p-90) REVERT: A 513 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5706 (mtt90) REVERT: A 525 ASN cc_start: 0.5972 (OUTLIER) cc_final: 0.5602 (p0) REVERT: A 603 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5437 (p90) REVERT: A 683 ARG cc_start: 0.8391 (tmm160) cc_final: 0.8144 (tmm160) outliers start: 23 outliers final: 14 residues processed: 76 average time/residue: 0.0824 time to fit residues: 7.9775 Evaluate side-chains 81 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.211523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165632 restraints weight = 6044.854| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.00 r_work: 0.3337 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5429 Z= 0.111 Angle : 0.579 6.554 7391 Z= 0.282 Chirality : 0.038 0.153 809 Planarity : 0.004 0.065 912 Dihedral : 6.507 59.981 922 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.61 % Favored : 92.23 % Rotamer: Outliers : 3.93 % Allowed : 30.71 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.79 (0.35), residues: 618 helix: 0.82 (0.31), residues: 292 sheet: -0.69 (0.70), residues: 64 loop : -2.10 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.009 0.001 TYR A 322 PHE 0.010 0.001 PHE A 281 TRP 0.015 0.001 TRP A 315 HIS 0.007 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5424) covalent geometry : angle 0.57593 ( 7377) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.38207 ( 2) hydrogen bonds : bond 0.03717 ( 203) hydrogen bonds : angle 3.75608 ( 576) link_BETA1-4 : bond 0.00181 ( 1) link_BETA1-4 : angle 1.12599 ( 3) link_NAG-ASN : bond 0.00211 ( 3) link_NAG-ASN : angle 1.72110 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5308 (ptt90) REVERT: A 50 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7910 (mtp180) REVERT: A 264 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6591 (mt) REVERT: A 318 LYS cc_start: 0.7431 (mttt) cc_final: 0.7022 (mmtt) REVERT: A 462 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5344 (pm20) REVERT: A 501 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.6574 (p-90) REVERT: A 513 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5674 (mtt90) REVERT: A 525 ASN cc_start: 0.6038 (OUTLIER) cc_final: 0.5690 (p0) REVERT: A 603 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5420 (p90) REVERT: A 683 ARG cc_start: 0.8389 (tmm160) cc_final: 0.8138 (tmm160) REVERT: A 724 ASN cc_start: 0.8089 (t0) cc_final: 0.7743 (m110) outliers start: 22 outliers final: 14 residues processed: 76 average time/residue: 0.0905 time to fit residues: 8.6192 Evaluate side-chains 80 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 501 TRP Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 603 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162060 restraints weight = 6071.262| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.33 r_work: 0.3323 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5429 Z= 0.138 Angle : 0.601 6.501 7391 Z= 0.293 Chirality : 0.039 0.153 809 Planarity : 0.004 0.065 912 Dihedral : 6.565 59.634 922 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.61 % Favored : 92.23 % Rotamer: Outliers : 3.93 % Allowed : 31.25 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.87 (0.35), residues: 618 helix: 0.78 (0.31), residues: 292 sheet: -0.80 (0.69), residues: 64 loop : -2.13 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.010 0.001 TYR A 322 PHE 0.011 0.001 PHE A 212 TRP 0.016 0.001 TRP A 315 HIS 0.010 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5424) covalent geometry : angle 0.59761 ( 7377) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.38821 ( 2) hydrogen bonds : bond 0.04067 ( 203) hydrogen bonds : angle 3.82993 ( 576) link_BETA1-4 : bond 0.00093 ( 1) link_BETA1-4 : angle 1.15979 ( 3) link_NAG-ASN : bond 0.00153 ( 3) link_NAG-ASN : angle 1.86627 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.31 seconds wall clock time: 24 minutes 15.22 seconds (1455.22 seconds total)