Starting phenix.real_space_refine on Wed Mar 12 08:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8z_44363/03_2025/9b8z_44363.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 V 10 8.30 5 S 39 5.16 5 C 4845 2.51 5 N 1309 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7469 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 221 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.44, per 1000 atoms: 0.72 Number of scatterers: 7509 At special positions: 0 Unit cell: (95.22, 115.092, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 10 22.97 Ca 2 19.99 S 39 16.00 O 1304 8.00 N 1309 7.00 C 4845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " 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 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 893.3 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.549A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.797A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.050A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.795A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.618A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1172 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.480A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.303A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 3297 1.45 - 1.67: 4295 1.67 - 1.89: 75 1.89 - 2.11: 28 2.11 - 2.33: 8 Bond restraints: 7703 Sorted by residual: bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.56e+00 bond pdb=" CB TRP A 820 " pdb=" CG TRP A 820 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.63e-01 bond pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.81e-01 bond pdb=" CB TRP A 565 " pdb=" CG TRP A 565 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.61e-01 bond pdb=" CB TRP A1124 " pdb=" CG TRP A1124 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.41e-01 ... (remaining 7698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 10147 0.98 - 1.96: 371 1.96 - 2.95: 39 2.95 - 3.93: 31 3.93 - 4.91: 11 Bond angle restraints: 10599 Sorted by residual: angle pdb=" CA TRP A1058 " pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 113.60 109.40 4.20 1.90e+00 2.77e-01 4.89e+00 angle pdb=" C PRO A 340 " pdb=" N LYS A 341 " pdb=" CA LYS A 341 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.51e+00 angle pdb=" C GLY A 306 " pdb=" N ALA A 307 " pdb=" CA ALA A 307 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" C ARG A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta sigma weight residual 122.60 119.09 3.51 1.88e+00 2.83e-01 3.49e+00 angle pdb=" CA TYR A1063 " pdb=" CB TYR A1063 " pdb=" CG TYR A1063 " ideal model delta sigma weight residual 113.90 110.64 3.26 1.80e+00 3.09e-01 3.28e+00 ... (remaining 10594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 4238 15.68 - 31.36: 197 31.36 - 47.04: 53 47.04 - 62.72: 13 62.72 - 78.40: 1 Dihedral angle restraints: 4502 sinusoidal: 1694 harmonic: 2808 Sorted by residual: dihedral pdb=" CA HIS A 447 " pdb=" C HIS A 447 " pdb=" N GLY A 448 " pdb=" CA GLY A 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sinusoidal sigma weight residual -60.00 -117.47 57.47 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA ARG A 571 " pdb=" CB ARG A 571 " pdb=" CG ARG A 571 " pdb=" CD ARG A 571 " ideal model delta sinusoidal sigma weight residual 180.00 125.98 54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 795 0.028 - 0.056: 286 0.056 - 0.084: 73 0.084 - 0.113: 32 0.113 - 0.141: 7 Chirality restraints: 1193 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA PRO A 779 " pdb=" N PRO A 779 " pdb=" C PRO A 779 " pdb=" CB PRO A 779 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL A 188 " pdb=" N VAL A 188 " pdb=" C VAL A 188 " pdb=" CB VAL A 188 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1190 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 457 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 603 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 604 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1029 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C LEU A1029 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU A1029 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL A1030 " -0.007 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 60 2.59 - 3.17: 6817 3.17 - 3.75: 11738 3.75 - 4.32: 14991 4.32 - 4.90: 26029 Nonbonded interactions: 59635 Sorted by model distance: nonbonded pdb=" O ARG A 353 " pdb=" OG1 THR A 356 " model vdw 2.014 3.040 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.120 2.510 nonbonded pdb=" NH1 ARG A 195 " pdb=" O PRO A 217 " model vdw 2.209 3.120 nonbonded pdb=" N GLN A 419 " pdb=" OE1 GLN A 419 " model vdw 2.223 3.120 nonbonded pdb=" OE1 GLU A 608 " pdb=" NH1 ARG A 611 " model vdw 2.225 3.120 ... (remaining 59630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7703 Z= 0.289 Angle : 0.476 4.908 10599 Z= 0.262 Chirality : 0.034 0.141 1193 Planarity : 0.003 0.046 1309 Dihedral : 10.452 78.404 2683 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.54 % Allowed : 4.73 % Favored : 94.73 % 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: 2.44 (0.29), residues: 958 helix: 2.80 (0.22), residues: 608 sheet: -0.17 (0.80), residues: 50 loop : -0.63 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 PHE 0.012 0.001 PHE A 931 TYR 0.008 0.001 TYR A1063 ARG 0.002 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.759 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.8865 (mmm) cc_final: 0.8559 (mmm) REVERT: A 622 MET cc_start: 0.8045 (mtp) cc_final: 0.7655 (mtp) REVERT: A 804 ASP cc_start: 0.7958 (t0) cc_final: 0.7630 (t0) REVERT: A 818 TYR cc_start: 0.8743 (m-10) cc_final: 0.8525 (m-80) REVERT: A 827 GLU cc_start: 0.8275 (tp30) cc_final: 0.8012 (tp30) REVERT: A 877 LEU cc_start: 0.9169 (mt) cc_final: 0.8804 (mt) REVERT: A 884 THR cc_start: 0.9186 (m) cc_final: 0.8636 (p) REVERT: A 1166 ARG cc_start: 0.4523 (ttp80) cc_final: 0.2372 (tpt170) outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 0.1678 time to fit residues: 33.4828 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.071897 restraints weight = 20980.066| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.36 r_work: 0.2954 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7703 Z= 0.216 Angle : 0.521 6.529 10599 Z= 0.270 Chirality : 0.038 0.170 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.472 15.895 1072 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.03 % Allowed : 11.22 % Favored : 86.76 % 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: 2.49 (0.29), residues: 958 helix: 2.82 (0.21), residues: 605 sheet: -0.16 (0.69), residues: 65 loop : -0.54 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.008 0.001 HIS A1128 PHE 0.013 0.001 PHE A 933 TYR 0.016 0.001 TYR A1168 ARG 0.007 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.865 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9116 (m) cc_final: 0.8843 (p) REVERT: A 186 MET cc_start: 0.9261 (mmm) cc_final: 0.8994 (mmm) REVERT: A 254 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8729 (mt-10) REVERT: A 378 LEU cc_start: 0.9440 (mt) cc_final: 0.9211 (mt) REVERT: A 608 GLU cc_start: 0.8474 (tp30) cc_final: 0.8255 (tp30) REVERT: A 804 ASP cc_start: 0.8479 (t0) cc_final: 0.8208 (t0) REVERT: A 818 TYR cc_start: 0.8968 (m-10) cc_final: 0.8684 (m-80) REVERT: A 827 GLU cc_start: 0.8873 (tp30) cc_final: 0.8513 (tp30) REVERT: A 884 THR cc_start: 0.9046 (m) cc_final: 0.8582 (p) REVERT: A 900 MET cc_start: 0.9042 (ttp) cc_final: 0.8485 (tpt) REVERT: A 1166 ARG cc_start: 0.4884 (ttp80) cc_final: 0.2276 (tpt170) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.1573 time to fit residues: 25.9092 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.071073 restraints weight = 21408.398| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.38 r_work: 0.2936 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7703 Z= 0.248 Angle : 0.518 8.186 10599 Z= 0.264 Chirality : 0.038 0.137 1193 Planarity : 0.004 0.050 1309 Dihedral : 3.474 15.822 1072 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.70 % Allowed : 13.24 % Favored : 84.05 % 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: 2.39 (0.29), residues: 958 helix: 2.83 (0.21), residues: 603 sheet: -0.31 (0.68), residues: 65 loop : -0.75 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.007 0.001 HIS A1128 PHE 0.009 0.001 PHE A 931 TYR 0.017 0.001 TYR A1168 ARG 0.003 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.798 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9132 (m) cc_final: 0.8854 (p) REVERT: A 186 MET cc_start: 0.9283 (mmm) cc_final: 0.9007 (mmm) REVERT: A 378 LEU cc_start: 0.9485 (mt) cc_final: 0.9259 (mt) REVERT: A 581 MET cc_start: 0.9081 (ptp) cc_final: 0.8785 (ptp) REVERT: A 818 TYR cc_start: 0.9041 (m-10) cc_final: 0.8782 (m-80) REVERT: A 827 GLU cc_start: 0.8850 (tp30) cc_final: 0.8557 (tp30) REVERT: A 900 MET cc_start: 0.9043 (ttp) cc_final: 0.8336 (tpt) REVERT: A 1166 ARG cc_start: 0.4958 (ttp80) cc_final: 0.2351 (tpt170) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 0.1527 time to fit residues: 25.0029 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 75 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.070272 restraints weight = 21352.251| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.35 r_work: 0.2916 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7703 Z= 0.273 Angle : 0.529 7.685 10599 Z= 0.268 Chirality : 0.038 0.128 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.528 16.584 1072 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.51 % Allowed : 14.05 % Favored : 82.43 % 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: 2.29 (0.29), residues: 958 helix: 2.78 (0.21), residues: 602 sheet: -0.21 (0.68), residues: 63 loop : -0.88 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.007 0.001 HIS A1128 PHE 0.017 0.001 PHE A 902 TYR 0.018 0.001 TYR A1168 ARG 0.003 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.826 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9169 (m) cc_final: 0.8871 (p) REVERT: A 355 MET cc_start: 0.9625 (mmp) cc_final: 0.9424 (mmm) REVERT: A 608 GLU cc_start: 0.8816 (mp0) cc_final: 0.8562 (mp0) REVERT: A 629 GLU cc_start: 0.9265 (mm-30) cc_final: 0.9010 (mm-30) REVERT: A 818 TYR cc_start: 0.9034 (m-10) cc_final: 0.8794 (m-80) REVERT: A 827 GLU cc_start: 0.8994 (tp30) cc_final: 0.8636 (tp30) REVERT: A 884 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 900 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8307 (tpt) REVERT: A 1166 ARG cc_start: 0.5020 (ttp80) cc_final: 0.2296 (tpt170) outliers start: 26 outliers final: 14 residues processed: 114 average time/residue: 0.1572 time to fit residues: 26.1370 Evaluate side-chains 102 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.087249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070437 restraints weight = 21073.094| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.32 r_work: 0.2924 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7703 Z= 0.222 Angle : 0.520 7.342 10599 Z= 0.259 Chirality : 0.037 0.125 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.506 17.339 1072 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.38 % Allowed : 14.59 % Favored : 82.03 % 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: 2.30 (0.29), residues: 958 helix: 2.79 (0.21), residues: 604 sheet: -0.21 (0.69), residues: 63 loop : -0.92 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 PHE 0.010 0.001 PHE A 902 TYR 0.018 0.001 TYR A1168 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.890 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9156 (m) cc_final: 0.8856 (p) REVERT: A 355 MET cc_start: 0.9607 (mmp) cc_final: 0.9390 (mmm) REVERT: A 581 MET cc_start: 0.9084 (ptp) cc_final: 0.8845 (ptp) REVERT: A 608 GLU cc_start: 0.8838 (mp0) cc_final: 0.8479 (mp0) REVERT: A 629 GLU cc_start: 0.9261 (mm-30) cc_final: 0.9012 (mm-30) REVERT: A 818 TYR cc_start: 0.9016 (m-10) cc_final: 0.8784 (m-80) REVERT: A 827 GLU cc_start: 0.8989 (tp30) cc_final: 0.8619 (tp30) REVERT: A 900 MET cc_start: 0.8978 (ttp) cc_final: 0.8278 (tpt) REVERT: A 1166 ARG cc_start: 0.5031 (ttp80) cc_final: 0.2396 (tpt170) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.1647 time to fit residues: 26.2744 Evaluate side-chains 102 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.071254 restraints weight = 21163.269| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.33 r_work: 0.2940 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7703 Z= 0.185 Angle : 0.506 7.765 10599 Z= 0.252 Chirality : 0.036 0.133 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.456 17.341 1072 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.11 % Allowed : 16.22 % Favored : 80.68 % 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: 2.30 (0.29), residues: 958 helix: 2.80 (0.21), residues: 604 sheet: -0.28 (0.70), residues: 64 loop : -0.92 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 PHE 0.010 0.001 PHE A 902 TYR 0.018 0.001 TYR A1168 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.822 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9180 (m) cc_final: 0.8880 (p) REVERT: A 355 MET cc_start: 0.9607 (mmp) cc_final: 0.9382 (mmm) REVERT: A 581 MET cc_start: 0.9098 (ptp) cc_final: 0.8817 (ptp) REVERT: A 608 GLU cc_start: 0.8866 (mp0) cc_final: 0.8547 (mp0) REVERT: A 827 GLU cc_start: 0.8998 (tp30) cc_final: 0.8609 (tp30) REVERT: A 900 MET cc_start: 0.8955 (ttp) cc_final: 0.8246 (tpt) REVERT: A 1166 ARG cc_start: 0.5195 (ttp80) cc_final: 0.2524 (tpt170) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 0.1645 time to fit residues: 25.4912 Evaluate side-chains 100 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071934 restraints weight = 20982.253| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.32 r_work: 0.2945 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7703 Z= 0.189 Angle : 0.530 15.014 10599 Z= 0.257 Chirality : 0.037 0.144 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.410 17.174 1072 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.73 % 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: 2.29 (0.29), residues: 958 helix: 2.81 (0.21), residues: 603 sheet: -0.38 (0.69), residues: 64 loop : -0.94 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.035 0.001 TYR A 818 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.905 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9181 (m) cc_final: 0.8884 (p) REVERT: A 355 MET cc_start: 0.9617 (mmp) cc_final: 0.9396 (mmm) REVERT: A 581 MET cc_start: 0.9084 (ptp) cc_final: 0.8786 (ptp) REVERT: A 608 GLU cc_start: 0.8888 (mp0) cc_final: 0.8521 (mp0) REVERT: A 644 ARG cc_start: 0.5818 (mmt180) cc_final: 0.5458 (tpt170) REVERT: A 827 GLU cc_start: 0.9017 (tp30) cc_final: 0.8621 (tp30) REVERT: A 900 MET cc_start: 0.8956 (ttp) cc_final: 0.8204 (tpt) REVERT: A 1166 ARG cc_start: 0.5302 (ttp80) cc_final: 0.2545 (tpt170) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 0.1670 time to fit residues: 25.9622 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070957 restraints weight = 21332.387| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.37 r_work: 0.2946 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7703 Z= 0.194 Angle : 0.509 6.988 10599 Z= 0.254 Chirality : 0.036 0.125 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.416 17.059 1072 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.70 % Allowed : 17.30 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.29), residues: 958 helix: 2.80 (0.21), residues: 603 sheet: -0.47 (0.69), residues: 64 loop : -0.94 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.010 0.001 PHE A 627 TYR 0.019 0.001 TYR A1168 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.853 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9184 (m) cc_final: 0.8871 (p) REVERT: A 581 MET cc_start: 0.9090 (ptp) cc_final: 0.8781 (ptp) REVERT: A 608 GLU cc_start: 0.8899 (mp0) cc_final: 0.8562 (mp0) REVERT: A 644 ARG cc_start: 0.5845 (mmt180) cc_final: 0.5455 (tpt170) REVERT: A 827 GLU cc_start: 0.9024 (tp30) cc_final: 0.8617 (tp30) REVERT: A 900 MET cc_start: 0.8964 (ttp) cc_final: 0.8209 (tpt) REVERT: A 1166 ARG cc_start: 0.5262 (ttp80) cc_final: 0.2559 (tpt170) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1526 time to fit residues: 23.1513 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071530 restraints weight = 21335.952| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.36 r_work: 0.2959 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7703 Z= 0.180 Angle : 0.531 13.307 10599 Z= 0.258 Chirality : 0.036 0.147 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.413 17.029 1072 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.57 % Allowed : 18.11 % Favored : 79.32 % 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: 2.22 (0.29), residues: 958 helix: 2.77 (0.21), residues: 603 sheet: -0.55 (0.68), residues: 64 loop : -0.94 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.019 0.001 TYR A1168 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.811 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9155 (m) cc_final: 0.8844 (p) REVERT: A 186 MET cc_start: 0.9288 (mmm) cc_final: 0.9060 (mmm) REVERT: A 581 MET cc_start: 0.9089 (ptp) cc_final: 0.8774 (ptp) REVERT: A 608 GLU cc_start: 0.8892 (mp0) cc_final: 0.8543 (mp0) REVERT: A 644 ARG cc_start: 0.5887 (mmt180) cc_final: 0.5466 (tpt170) REVERT: A 827 GLU cc_start: 0.9018 (tp30) cc_final: 0.8609 (tp30) REVERT: A 900 MET cc_start: 0.8944 (ttp) cc_final: 0.8180 (tpt) REVERT: A 1166 ARG cc_start: 0.5339 (ttp80) cc_final: 0.2576 (tpt170) outliers start: 19 outliers final: 16 residues processed: 100 average time/residue: 0.1490 time to fit residues: 22.0942 Evaluate side-chains 100 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 65 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072924 restraints weight = 21325.562| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.37 r_work: 0.2989 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7703 Z= 0.147 Angle : 0.523 11.862 10599 Z= 0.255 Chirality : 0.037 0.367 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.377 16.834 1072 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.30 % Allowed : 18.38 % Favored : 79.32 % 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: 2.21 (0.29), residues: 958 helix: 2.74 (0.21), residues: 604 sheet: -0.57 (0.68), residues: 64 loop : -0.92 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.019 0.001 TYR A1168 ARG 0.002 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.044 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9125 (m) cc_final: 0.8796 (p) REVERT: A 186 MET cc_start: 0.9256 (mmm) cc_final: 0.9021 (mmm) REVERT: A 581 MET cc_start: 0.9100 (ptp) cc_final: 0.8793 (ptp) REVERT: A 608 GLU cc_start: 0.8867 (mp0) cc_final: 0.8557 (mp0) REVERT: A 644 ARG cc_start: 0.5846 (mmt180) cc_final: 0.5422 (tpt170) REVERT: A 827 GLU cc_start: 0.8975 (tp30) cc_final: 0.8569 (tp30) REVERT: A 900 MET cc_start: 0.8898 (ttp) cc_final: 0.8091 (tpt) REVERT: A 1166 ARG cc_start: 0.5272 (ttp80) cc_final: 0.2540 (tpt170) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.1682 time to fit residues: 25.7332 Evaluate side-chains 99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.072712 restraints weight = 21045.938| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.38 r_work: 0.2988 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7703 Z= 0.159 Angle : 0.535 11.927 10599 Z= 0.259 Chirality : 0.038 0.309 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.371 16.673 1072 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.57 % Allowed : 19.19 % Favored : 78.24 % 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: 2.15 (0.28), residues: 958 helix: 2.75 (0.21), residues: 597 sheet: -0.58 (0.68), residues: 64 loop : -0.97 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.028 0.001 TYR A 818 ARG 0.007 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.38 seconds wall clock time: 60 minutes 27.53 seconds (3627.53 seconds total)