Starting phenix.real_space_refine on Tue Feb 11 14:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg4_37502/02_2025/8wg4_37502.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.067 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 1 5.49 5 S 46 5.16 5 C 3940 2.51 5 N 923 2.21 5 O 977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5887 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5597 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 661} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 290 Unusual residues: {'LBN': 1, 'Y01': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 3.90, per 1000 atoms: 0.66 Number of scatterers: 5887 At special positions: 0 Unit cell: (88.7062, 88.7062, 104.269, 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 46 16.00 P 1 15.00 O 977 8.00 N 923 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 559 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 829.1 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 39 removed outlier: 4.469A pdb=" N GLY A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 40 through 66 removed outlier: 4.003A pdb=" N ALA A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.649A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 145 through 172 removed outlier: 3.715A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.553A pdb=" N VAL A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 removed outlier: 5.670A pdb=" N ILE A 195 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 231 removed outlier: 3.612A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.532A pdb=" N LYS A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.708A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.721A pdb=" N LYS A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 331 through 355 removed outlier: 4.313A pdb=" N ASN A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 421 through 426 removed outlier: 5.068A pdb=" N ARG A 426 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.560A pdb=" N TRP A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.650A pdb=" N ILE A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.515A pdb=" N TYR A 469 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 497 removed outlier: 3.730A pdb=" N GLN A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 506 through 527 Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 553 through 561 removed outlier: 4.108A pdb=" N CYS A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 560 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 578 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 619 through 641 removed outlier: 3.554A pdb=" N CYS A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 666 removed outlier: 4.543A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 703 removed outlier: 3.736A pdb=" N VAL A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A 683 " --> pdb=" O GLY A 679 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.629A pdb=" N PHE A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 730 removed outlier: 3.506A pdb=" N THR A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 717 " --> pdb=" O THR A 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 276 removed outlier: 5.300A pdb=" N MET A 361 " --> pdb=" O CYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 383 through 384 349 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 884 1.32 - 1.44: 1649 1.44 - 1.57: 3456 1.57 - 1.70: 2 1.70 - 1.83: 66 Bond restraints: 6057 Sorted by residual: bond pdb=" CE1 HIS A 157 " pdb=" NE2 HIS A 157 " ideal model delta sigma weight residual 1.321 1.272 0.049 1.00e-02 1.00e+04 2.36e+01 bond pdb=" CG HIS A 157 " pdb=" CD2 HIS A 157 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" C LEU A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.25e-02 6.40e+03 7.34e+00 bond pdb=" C9 LBN A1201 " pdb=" O2 LBN A1201 " ideal model delta sigma weight residual 1.409 1.462 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CA SER A 699 " pdb=" CB SER A 699 " ideal model delta sigma weight residual 1.528 1.488 0.041 1.56e-02 4.11e+03 6.75e+00 ... (remaining 6052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 7432 2.30 - 4.59: 772 4.59 - 6.89: 31 6.89 - 9.19: 3 9.19 - 11.48: 1 Bond angle restraints: 8239 Sorted by residual: angle pdb=" CA ASN A 197 " pdb=" CB ASN A 197 " pdb=" CG ASN A 197 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CA PHE A 479 " pdb=" CB PHE A 479 " pdb=" CG PHE A 479 " ideal model delta sigma weight residual 113.80 118.28 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA TYR A 637 " pdb=" CB TYR A 637 " pdb=" CG TYR A 637 " ideal model delta sigma weight residual 113.90 105.89 8.01 1.80e+00 3.09e-01 1.98e+01 angle pdb=" CA HIS A 613 " pdb=" CB HIS A 613 " pdb=" CG HIS A 613 " ideal model delta sigma weight residual 113.80 109.38 4.42 1.00e+00 1.00e+00 1.95e+01 angle pdb=" C TYR A 264 " pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " ideal model delta sigma weight residual 108.88 115.37 -6.49 1.50e+00 4.44e-01 1.87e+01 ... (remaining 8234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 3708 23.41 - 46.82: 171 46.82 - 70.24: 30 70.24 - 93.65: 6 93.65 - 117.06: 5 Dihedral angle restraints: 3920 sinusoidal: 1887 harmonic: 2033 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -150.81 64.81 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ARG A 29 " pdb=" CA ARG A 29 " ideal model delta harmonic sigma weight residual 180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP A 181 " pdb=" C ASP A 181 " pdb=" N LEU A 182 " pdb=" CA LEU A 182 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 588 0.070 - 0.139: 285 0.139 - 0.209: 51 0.209 - 0.278: 7 0.278 - 0.348: 1 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA ASN A 306 " pdb=" N ASN A 306 " pdb=" C ASN A 306 " pdb=" CB ASN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASN A 438 " pdb=" N ASN A 438 " pdb=" C ASN A 438 " pdb=" CB ASN A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 374 " pdb=" CA ILE A 374 " pdb=" CG1 ILE A 374 " pdb=" CG2 ILE A 374 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 929 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 637 " -0.100 2.00e-02 2.50e+03 5.18e-02 5.37e+01 pdb=" CG TYR A 637 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 637 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 637 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 637 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 637 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 637 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 637 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A1207 " -0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" CAY Y01 A1207 " 0.071 2.00e-02 2.50e+03 pdb=" OAG Y01 A1207 " -0.029 2.00e-02 2.50e+03 pdb=" OAW Y01 A1207 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.048 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 69 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.021 2.00e-02 2.50e+03 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1775 2.86 - 3.37: 5663 3.37 - 3.88: 8983 3.88 - 4.39: 10345 4.39 - 4.90: 17873 Nonbonded interactions: 44639 Sorted by model distance: nonbonded pdb=" ND2 ASN A 682 " pdb=" OAG Y01 A1207 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG A 512 " pdb=" OAH Y01 A1207 " model vdw 2.437 3.120 nonbonded pdb=" OH TYR A 151 " pdb=" OD2 ASP A 659 " model vdw 2.530 3.040 nonbonded pdb=" OH TYR A 264 " pdb=" OD2 ASP A 378 " model vdw 2.577 3.040 nonbonded pdb=" O LEU A 527 " pdb=" OG SER A 531 " model vdw 2.589 3.040 ... (remaining 44634 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 group one per residue 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: 0.280 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.009 0.053 6057 Z= 0.557 Angle : 1.360 11.484 8239 Z= 0.899 Chirality : 0.078 0.348 932 Planarity : 0.011 0.097 974 Dihedral : 14.668 117.059 2603 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.82 % Allowed : 6.12 % Favored : 92.07 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.29), residues: 679 helix: -1.68 (0.20), residues: 446 sheet: 0.57 (1.30), residues: 22 loop : -1.33 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.007 TRP A 206 HIS 0.025 0.005 HIS A 226 PHE 0.035 0.007 PHE A 154 TYR 0.100 0.009 TYR A 637 ARG 0.015 0.003 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.592 Fit side-chains REVERT: A 69 TYR cc_start: 0.7908 (p90) cc_final: 0.7464 (p90) REVERT: A 143 LYS cc_start: 0.6429 (tptp) cc_final: 0.6045 (tptp) REVERT: A 181 ASP cc_start: 0.7692 (m-30) cc_final: 0.7461 (t0) REVERT: A 237 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5591 (tp) REVERT: A 241 THR cc_start: 0.9239 (m) cc_final: 0.8906 (p) REVERT: A 252 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6839 (mp0) REVERT: A 254 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7522 (tp30) REVERT: A 310 MET cc_start: 0.6816 (mpt) cc_final: 0.6315 (mpp) REVERT: A 335 TYR cc_start: 0.7170 (t80) cc_final: 0.6755 (t80) REVERT: A 349 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6907 (mmm160) REVERT: A 445 LEU cc_start: 0.5617 (mt) cc_final: 0.5380 (mt) REVERT: A 548 LYS cc_start: 0.6310 (mtmm) cc_final: 0.6083 (pttt) REVERT: A 676 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 706 LEU cc_start: 0.8188 (mt) cc_final: 0.7952 (pp) REVERT: A 740 ASN cc_start: 0.6817 (t0) cc_final: 0.6609 (t0) outliers start: 11 outliers final: 2 residues processed: 107 average time/residue: 0.1928 time to fit residues: 26.7253 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 676 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 197 ASN A 202 ASN A 516 HIS A 565 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121843 restraints weight = 6796.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124307 restraints weight = 4943.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125953 restraints weight = 4063.067| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6057 Z= 0.221 Angle : 0.665 8.887 8239 Z= 0.341 Chirality : 0.042 0.152 932 Planarity : 0.004 0.035 974 Dihedral : 10.146 79.967 1313 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.98 % Allowed : 10.74 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.32), residues: 679 helix: 0.58 (0.24), residues: 446 sheet: 2.37 (1.91), residues: 10 loop : -1.16 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.003 0.001 HIS A 259 PHE 0.021 0.002 PHE A 298 TYR 0.018 0.002 TYR A 637 ARG 0.004 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.613 Fit side-chains REVERT: A 205 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6575 (tt) REVERT: A 237 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7186 (tp) REVERT: A 292 GLU cc_start: 0.7364 (tt0) cc_final: 0.7041 (tt0) REVERT: A 445 LEU cc_start: 0.7161 (mt) cc_final: 0.6925 (mt) REVERT: A 609 ASN cc_start: 0.8209 (t0) cc_final: 0.7421 (t0) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1791 time to fit residues: 21.3973 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.162065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122674 restraints weight = 6855.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124175 restraints weight = 5152.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124553 restraints weight = 4108.506| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6057 Z= 0.234 Angle : 0.619 8.190 8239 Z= 0.312 Chirality : 0.041 0.155 932 Planarity : 0.004 0.038 974 Dihedral : 8.742 58.316 1311 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.14 % Allowed : 13.22 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 679 helix: 1.26 (0.24), residues: 447 sheet: 1.14 (1.78), residues: 10 loop : -1.27 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 431 HIS 0.003 0.001 HIS A 516 PHE 0.016 0.002 PHE A 730 TYR 0.016 0.002 TYR A 264 ARG 0.003 0.000 ARG A 608 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 181 ASP cc_start: 0.6831 (t0) cc_final: 0.6605 (t0) REVERT: A 310 MET cc_start: 0.6709 (mpp) cc_final: 0.6493 (mmt) REVERT: A 445 LEU cc_start: 0.7104 (mt) cc_final: 0.6851 (mt) REVERT: A 628 MET cc_start: 0.7287 (mmm) cc_final: 0.6983 (mmp) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1785 time to fit residues: 19.6170 Evaluate side-chains 77 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.162779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122430 restraints weight = 6921.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124658 restraints weight = 5083.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126212 restraints weight = 4200.182| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6057 Z= 0.220 Angle : 0.578 8.004 8239 Z= 0.289 Chirality : 0.039 0.135 932 Planarity : 0.004 0.040 974 Dihedral : 8.371 63.928 1307 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.47 % Allowed : 14.05 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.32), residues: 679 helix: 1.50 (0.24), residues: 448 sheet: 0.81 (1.67), residues: 10 loop : -1.33 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.003 0.001 HIS A 157 PHE 0.013 0.002 PHE A 549 TYR 0.022 0.001 TYR A 496 ARG 0.007 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: A 181 ASP cc_start: 0.6768 (t0) cc_final: 0.6074 (t0) REVERT: A 282 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: A 335 TYR cc_start: 0.7457 (t80) cc_final: 0.6792 (t80) REVERT: A 445 LEU cc_start: 0.7086 (mt) cc_final: 0.6822 (mt) REVERT: A 628 MET cc_start: 0.7853 (mmm) cc_final: 0.7194 (mmp) outliers start: 21 outliers final: 16 residues processed: 84 average time/residue: 0.1684 time to fit residues: 18.9774 Evaluate side-chains 84 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.164918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124076 restraints weight = 6876.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126671 restraints weight = 4830.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128416 restraints weight = 3893.487| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6057 Z= 0.167 Angle : 0.543 7.814 8239 Z= 0.268 Chirality : 0.038 0.135 932 Planarity : 0.004 0.041 974 Dihedral : 8.107 67.290 1307 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.30 % Allowed : 15.37 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.33), residues: 679 helix: 1.79 (0.25), residues: 447 sheet: 0.42 (1.59), residues: 10 loop : -1.24 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 128 HIS 0.002 0.001 HIS A 259 PHE 0.014 0.001 PHE A 549 TYR 0.018 0.001 TYR A 496 ARG 0.006 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: A 181 ASP cc_start: 0.6720 (t0) cc_final: 0.6453 (t70) REVERT: A 282 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: A 445 LEU cc_start: 0.7007 (mt) cc_final: 0.6747 (mt) REVERT: A 606 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7249 (mp0) outliers start: 26 outliers final: 18 residues processed: 94 average time/residue: 0.1872 time to fit residues: 23.1636 Evaluate side-chains 91 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.161048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120663 restraints weight = 6875.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122761 restraints weight = 5116.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124255 restraints weight = 4279.644| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6057 Z= 0.285 Angle : 0.601 7.247 8239 Z= 0.299 Chirality : 0.041 0.138 932 Planarity : 0.004 0.041 974 Dihedral : 8.356 70.890 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.45 % Allowed : 15.87 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.33), residues: 679 helix: 1.65 (0.25), residues: 450 sheet: 0.56 (1.67), residues: 10 loop : -1.29 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 431 HIS 0.005 0.001 HIS A 157 PHE 0.016 0.002 PHE A 154 TYR 0.016 0.002 TYR A 496 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: A 181 ASP cc_start: 0.6659 (t0) cc_final: 0.6426 (t70) REVERT: A 282 MET cc_start: 0.8534 (mtm) cc_final: 0.8228 (mtm) REVERT: A 383 LYS cc_start: 0.7425 (ptpt) cc_final: 0.6566 (mttp) REVERT: A 445 LEU cc_start: 0.7142 (mt) cc_final: 0.6855 (mt) REVERT: A 727 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6493 (t-90) outliers start: 33 outliers final: 25 residues processed: 93 average time/residue: 0.1600 time to fit residues: 20.3585 Evaluate side-chains 97 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.162742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124759 restraints weight = 6895.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126150 restraints weight = 4841.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126534 restraints weight = 4001.323| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6057 Z= 0.188 Angle : 0.550 8.154 8239 Z= 0.270 Chirality : 0.038 0.135 932 Planarity : 0.004 0.041 974 Dihedral : 8.114 72.736 1307 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.96 % Allowed : 16.69 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.33), residues: 679 helix: 1.85 (0.25), residues: 450 sheet: 0.26 (1.61), residues: 10 loop : -1.12 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 431 HIS 0.002 0.001 HIS A 157 PHE 0.012 0.001 PHE A 549 TYR 0.017 0.001 TYR A 496 ARG 0.001 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6954 (m-80) REVERT: A 282 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8172 (mtm) REVERT: A 383 LYS cc_start: 0.7247 (ptpt) cc_final: 0.6404 (mttp) REVERT: A 445 LEU cc_start: 0.7100 (mt) cc_final: 0.6822 (mt) REVERT: A 583 MET cc_start: 0.7603 (mmm) cc_final: 0.7317 (mmt) REVERT: A 606 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 30 outliers final: 24 residues processed: 92 average time/residue: 0.1691 time to fit residues: 21.1263 Evaluate side-chains 98 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 41 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.164251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124696 restraints weight = 6808.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127029 restraints weight = 4891.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128474 restraints weight = 4036.372| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6057 Z= 0.165 Angle : 0.536 8.651 8239 Z= 0.260 Chirality : 0.038 0.132 932 Planarity : 0.003 0.041 974 Dihedral : 7.859 73.174 1307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.63 % Allowed : 17.52 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.33), residues: 679 helix: 2.00 (0.25), residues: 451 sheet: 0.13 (1.60), residues: 10 loop : -1.06 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 626 HIS 0.002 0.001 HIS A 516 PHE 0.016 0.001 PHE A 549 TYR 0.016 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 178 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: A 348 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6883 (ttm110) REVERT: A 383 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6440 (mttp) REVERT: A 445 LEU cc_start: 0.7101 (mt) cc_final: 0.6804 (mt) REVERT: A 583 MET cc_start: 0.7587 (mmm) cc_final: 0.7307 (mmt) outliers start: 28 outliers final: 20 residues processed: 93 average time/residue: 0.1633 time to fit residues: 20.6556 Evaluate side-chains 96 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.162421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122408 restraints weight = 6964.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124640 restraints weight = 5053.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126289 restraints weight = 4160.012| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6057 Z= 0.208 Angle : 0.554 7.669 8239 Z= 0.270 Chirality : 0.039 0.133 932 Planarity : 0.004 0.041 974 Dihedral : 7.847 73.010 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.80 % Allowed : 18.84 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.33), residues: 679 helix: 1.96 (0.25), residues: 449 sheet: 0.12 (1.60), residues: 10 loop : -1.08 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 431 HIS 0.002 0.001 HIS A 157 PHE 0.016 0.001 PHE A 549 TYR 0.015 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6902 (ttm110) REVERT: A 383 LYS cc_start: 0.7060 (ptpt) cc_final: 0.6459 (mttp) REVERT: A 445 LEU cc_start: 0.7097 (mt) cc_final: 0.6799 (mt) REVERT: A 583 MET cc_start: 0.7579 (mmm) cc_final: 0.7300 (mmt) outliers start: 23 outliers final: 20 residues processed: 85 average time/residue: 0.1565 time to fit residues: 18.1062 Evaluate side-chains 91 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125484 restraints weight = 6959.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126807 restraints weight = 4973.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126901 restraints weight = 4044.911| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6057 Z= 0.191 Angle : 0.546 7.754 8239 Z= 0.266 Chirality : 0.038 0.133 932 Planarity : 0.003 0.041 974 Dihedral : 7.713 73.620 1307 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.46 % Allowed : 17.85 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 679 helix: 1.97 (0.25), residues: 450 sheet: 0.03 (1.59), residues: 10 loop : -1.09 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 420 HIS 0.003 0.001 HIS A 157 PHE 0.015 0.001 PHE A 549 TYR 0.015 0.001 TYR A 496 ARG 0.002 0.000 ARG A 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6929 (ttm110) REVERT: A 383 LYS cc_start: 0.7008 (ptpt) cc_final: 0.6340 (mttp) REVERT: A 445 LEU cc_start: 0.7128 (mt) cc_final: 0.6831 (mt) REVERT: A 583 MET cc_start: 0.7581 (mmm) cc_final: 0.7311 (mmt) outliers start: 27 outliers final: 24 residues processed: 89 average time/residue: 0.1537 time to fit residues: 18.8924 Evaluate side-chains 94 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 411 TYR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 737 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.162695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124547 restraints weight = 6985.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126362 restraints weight = 4928.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126608 restraints weight = 3854.835| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6057 Z= 0.200 Angle : 0.555 7.460 8239 Z= 0.271 Chirality : 0.039 0.135 932 Planarity : 0.003 0.041 974 Dihedral : 7.693 73.830 1307 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.46 % Allowed : 17.85 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.33), residues: 679 helix: 1.97 (0.25), residues: 449 sheet: 0.01 (1.60), residues: 10 loop : -1.15 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 420 HIS 0.003 0.001 HIS A 739 PHE 0.015 0.001 PHE A 549 TYR 0.018 0.001 TYR A 335 ARG 0.002 0.000 ARG A 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.77 seconds wall clock time: 34 minutes 47.77 seconds (2087.77 seconds total)