Starting phenix.real_space_refine on Mon Apr 28 13:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8z_44363/04_2025/9b8z_44363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8z_44363/04_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_44363/04_2025/9b8z_44363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8z_44363/04_2025/9b8z_44363.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8z_44363/04_2025/9b8z_44363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8z_44363/04_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-5669/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: 4.94, per 1000 atoms: 0.66 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: 2.11 Conformation dependent library (CDL) restraints added in 886.2 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: 0.83 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: 2.27 Time building geometry restraints manager: 2.45 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.780 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- 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 7704 Z= 0.211 Angle : 0.476 4.908 10601 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 Details of bonding type rmsd hydrogen bonds : bond 0.12252 ( 473) hydrogen bonds : angle 5.01660 ( 1374) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.96705 ( 2) covalent geometry : bond 0.00446 ( 7703) covalent geometry : angle 0.47585 (10599) *********************** 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 : 0.818 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: 0.1704 time to fit residues: 34.1359 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 : 0.802 ------------------------------------------------------------------------------- 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 7704 Z= 0.144 Angle : 0.521 6.529 10601 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 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 473) hydrogen bonds : angle 4.18605 ( 1374) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.33250 ( 2) covalent geometry : bond 0.00325 ( 7703) covalent geometry : angle 0.52143 (10599) *********************** 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 : 0.883 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: 0.1606 time to fit residues: 26.6689 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 : 0.889 ------------------------------------------------------------------------------- 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: 0.0870 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: 1.0162 ------------------------------------------------------------------------------- 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 ** 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 = 0.3411 r_free = 0.3411 target = 0.088299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071339 restraints weight = 21406.225| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.39 r_work: 0.2942 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7704 Z= 0.153 Angle : 0.512 8.344 10601 Z= 0.261 Chirality : 0.038 0.143 1193 Planarity : 0.004 0.050 1309 Dihedral : 3.465 15.821 1072 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.70 % Allowed : 12.84 % Favored : 84.46 % 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: 2.40 (0.29), residues: 958 helix: 2.84 (0.21), residues: 603 sheet: -0.28 (0.68), residues: 65 loop : -0.74 (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 902 TYR 0.017 0.001 TYR A1168 ARG 0.003 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 473) hydrogen bonds : angle 4.08530 ( 1374) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.47273 ( 2) covalent geometry : bond 0.00352 ( 7703) covalent geometry : angle 0.51180 (10599) *********************** 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 117 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.833 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9117 (m) cc_final: 0.8835 (p) REVERT: A 186 MET cc_start: 0.9288 (mmm) cc_final: 0.9018 (mmm) REVERT: A 378 LEU cc_start: 0.9481 (mt) cc_final: 0.9260 (mt) REVERT: A 818 TYR cc_start: 0.9020 (m-10) cc_final: 0.8767 (m-80) REVERT: A 827 GLU cc_start: 0.8840 (tp30) cc_final: 0.8546 (tp30) REVERT: A 884 THR cc_start: 0.9048 (m) cc_final: 0.8563 (p) REVERT: A 900 MET cc_start: 0.9035 (ttp) cc_final: 0.8331 (tpt) REVERT: A 1166 ARG cc_start: 0.4935 (ttp80) cc_final: 0.2335 (tpt170) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.1525 time to fit residues: 25.1917 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 : 0.802 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 68 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072696 restraints weight = 21213.072| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.36 r_work: 0.2980 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7704 Z= 0.108 Angle : 0.492 8.013 10601 Z= 0.246 Chirality : 0.036 0.128 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.444 16.093 1072 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.84 % Allowed : 13.92 % Favored : 83.24 % 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: 2.33 (0.29), residues: 958 helix: 2.82 (0.21), residues: 600 sheet: -0.29 (0.68), residues: 65 loop : -0.82 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 PHE 0.020 0.001 PHE A 902 TYR 0.017 0.001 TYR A1168 ARG 0.002 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 473) hydrogen bonds : angle 3.93773 ( 1374) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.41670 ( 2) covalent geometry : bond 0.00238 ( 7703) covalent geometry : angle 0.49222 (10599) *********************** 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: 21 poor density : 99 time to evaluate : 0.813 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 9 SER cc_start: 0.8789 (m) cc_final: 0.8405 (t) REVERT: A 72 THR cc_start: 0.9112 (m) cc_final: 0.8832 (p) REVERT: A 186 MET cc_start: 0.9250 (mmm) cc_final: 0.9000 (mmp) REVERT: A 355 MET cc_start: 0.9595 (mmp) cc_final: 0.9369 (mmm) REVERT: A 608 GLU cc_start: 0.8722 (mp0) cc_final: 0.8415 (mp0) REVERT: A 818 TYR cc_start: 0.9006 (m-10) cc_final: 0.8788 (m-80) REVERT: A 827 GLU cc_start: 0.8924 (tp30) cc_final: 0.8571 (tp30) REVERT: A 884 THR cc_start: 0.8988 (m) cc_final: 0.8506 (p) REVERT: A 900 MET cc_start: 0.8980 (ttp) cc_final: 0.8268 (tpt) REVERT: A 1166 ARG cc_start: 0.5012 (ttp80) cc_final: 0.2362 (tpt170) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.1539 time to fit residues: 25.7637 Evaluate side-chains 108 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 869 LEU 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: 6.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.068982 restraints weight = 21253.741| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.29 r_work: 0.2894 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7704 Z= 0.255 Angle : 0.585 6.961 10601 Z= 0.296 Chirality : 0.039 0.135 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.554 16.834 1072 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.51 % Allowed : 14.46 % 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: 2.23 (0.29), residues: 958 helix: 2.77 (0.21), residues: 601 sheet: -0.32 (0.68), residues: 63 loop : -0.97 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.007 0.001 HIS A1128 PHE 0.013 0.001 PHE A 627 TYR 0.017 0.001 TYR A1168 ARG 0.003 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 473) hydrogen bonds : angle 4.15890 ( 1374) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.74086 ( 2) covalent geometry : bond 0.00581 ( 7703) covalent geometry : angle 0.58537 (10599) *********************** 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 114 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.915 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9242 (m) cc_final: 0.8934 (p) REVERT: A 355 MET cc_start: 0.9621 (mmp) cc_final: 0.9416 (mmm) REVERT: A 430 MET cc_start: 0.9183 (mmm) cc_final: 0.8976 (tpp) REVERT: A 608 GLU cc_start: 0.8858 (mp0) cc_final: 0.8509 (mp0) REVERT: A 818 TYR cc_start: 0.9049 (m-10) cc_final: 0.8818 (m-80) REVERT: A 827 GLU cc_start: 0.9043 (tp30) cc_final: 0.8721 (tp30) REVERT: A 881 CYS cc_start: 0.9179 (m) cc_final: 0.8698 (m) REVERT: A 884 THR cc_start: 0.9079 (m) cc_final: 0.8358 (p) REVERT: A 900 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8328 (tpt) REVERT: A 984 ASP cc_start: 0.8686 (t70) cc_final: 0.8405 (t0) REVERT: A 1166 ARG cc_start: 0.5180 (ttp80) cc_final: 0.2410 (tpt170) outliers start: 26 outliers final: 15 residues processed: 108 average time/residue: 0.1701 time to fit residues: 26.4738 Evaluate side-chains 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 900 MET Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1023 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: 3.9990 chunk 33 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071058 restraints weight = 21094.556| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.32 r_work: 0.2935 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7704 Z= 0.123 Angle : 0.515 7.825 10601 Z= 0.256 Chirality : 0.037 0.138 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.504 16.283 1072 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.84 % Allowed : 15.68 % Favored : 81.49 % 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: 2.24 (0.29), residues: 958 helix: 2.78 (0.21), residues: 602 sheet: -0.38 (0.69), residues: 64 loop : -0.95 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 PHE 0.017 0.001 PHE A 933 TYR 0.018 0.001 TYR A1168 ARG 0.002 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 473) hydrogen bonds : angle 3.99214 ( 1374) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.49254 ( 2) covalent geometry : bond 0.00275 ( 7703) covalent geometry : angle 0.51548 (10599) *********************** 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 118 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.823 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9193 (m) cc_final: 0.8894 (p) REVERT: A 355 MET cc_start: 0.9597 (mmp) cc_final: 0.9378 (mmm) REVERT: A 608 GLU cc_start: 0.8872 (mp0) cc_final: 0.8504 (mp0) REVERT: A 644 ARG cc_start: 0.5836 (mmt180) cc_final: 0.5457 (tpt170) REVERT: A 827 GLU cc_start: 0.8983 (tp30) cc_final: 0.8606 (tp30) REVERT: A 884 THR cc_start: 0.9007 (m) cc_final: 0.8516 (p) REVERT: A 900 MET cc_start: 0.8986 (ttp) cc_final: 0.8295 (tpt) REVERT: A 1166 ARG cc_start: 0.5133 (ttp80) cc_final: 0.2441 (tpt170) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.1687 time to fit residues: 27.2060 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 974 ILE 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: 1.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3391 r_free = 0.3391 target = 0.086799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.070024 restraints weight = 21132.507| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.28 r_work: 0.2918 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7704 Z= 0.176 Angle : 0.555 9.289 10601 Z= 0.273 Chirality : 0.037 0.126 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.486 16.175 1072 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.57 % Allowed : 16.76 % 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: 2.16 (0.29), residues: 958 helix: 2.73 (0.21), residues: 601 sheet: -0.49 (0.69), residues: 64 loop : -0.99 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 680 HIS 0.006 0.001 HIS A1128 PHE 0.011 0.001 PHE A 627 TYR 0.034 0.002 TYR A 818 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 473) hydrogen bonds : angle 4.07907 ( 1374) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.54914 ( 2) covalent geometry : bond 0.00405 ( 7703) covalent geometry : angle 0.55465 (10599) *********************** 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 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.821 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9171 (m) cc_final: 0.8861 (p) REVERT: A 608 GLU cc_start: 0.8902 (mp0) cc_final: 0.8553 (mp0) REVERT: A 644 ARG cc_start: 0.5796 (mmt180) cc_final: 0.5348 (tpt170) REVERT: A 827 GLU cc_start: 0.9031 (tp30) cc_final: 0.8640 (tp30) REVERT: A 884 THR cc_start: 0.9018 (m) cc_final: 0.8522 (p) REVERT: A 900 MET cc_start: 0.9006 (ttp) cc_final: 0.8287 (tpt) REVERT: A 1166 ARG cc_start: 0.5336 (ttp80) cc_final: 0.2565 (tpt170) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.1614 time to fit residues: 23.1275 Evaluate side-chains 93 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 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 974 ILE Chi-restraints excluded: chain A residue 1133 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: 0.9990 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3402 r_free = 0.3402 target = 0.087498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070526 restraints weight = 21254.432| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.37 r_work: 0.2929 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7704 Z= 0.143 Angle : 0.544 11.923 10601 Z= 0.266 Chirality : 0.037 0.155 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.459 15.093 1072 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.84 % Allowed : 17.03 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.28), residues: 958 helix: 2.73 (0.21), residues: 601 sheet: -0.57 (0.68), residues: 64 loop : -1.00 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.006 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 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 473) hydrogen bonds : angle 4.03277 ( 1374) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.55711 ( 2) covalent geometry : bond 0.00326 ( 7703) covalent geometry : angle 0.54403 (10599) *********************** 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: 21 poor density : 85 time to evaluate : 0.787 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9206 (m) cc_final: 0.8874 (p) REVERT: A 440 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 608 GLU cc_start: 0.8905 (mp0) cc_final: 0.8546 (mp0) REVERT: A 644 ARG cc_start: 0.5835 (mmt180) cc_final: 0.5363 (tpt170) REVERT: A 827 GLU cc_start: 0.9025 (tp30) cc_final: 0.8639 (tp30) REVERT: A 900 MET cc_start: 0.8970 (ttp) cc_final: 0.8237 (tpt) REVERT: A 1166 ARG cc_start: 0.5322 (ttp80) cc_final: 0.2562 (tpt170) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.1575 time to fit residues: 23.8590 Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 300 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 440 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.089047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.072142 restraints weight = 21284.968| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.38 r_work: 0.2966 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7704 Z= 0.108 Angle : 0.532 11.528 10601 Z= 0.258 Chirality : 0.036 0.125 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.413 13.995 1072 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 18.11 % 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: 2.14 (0.28), residues: 958 helix: 2.74 (0.21), residues: 601 sheet: -0.60 (0.68), residues: 64 loop : -1.00 (0.36), residues: 293 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 902 TYR 0.019 0.001 TYR A1168 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 473) hydrogen bonds : angle 3.94646 ( 1374) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.48704 ( 2) covalent geometry : bond 0.00238 ( 7703) covalent geometry : angle 0.53230 (10599) *********************** 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: 16 poor density : 88 time to evaluate : 0.814 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9141 (m) cc_final: 0.8825 (p) REVERT: A 608 GLU cc_start: 0.8894 (mp0) cc_final: 0.8570 (mp0) REVERT: A 644 ARG cc_start: 0.5787 (mmt180) cc_final: 0.5288 (tpt170) REVERT: A 827 GLU cc_start: 0.8981 (tp30) cc_final: 0.8586 (tp30) REVERT: A 900 MET cc_start: 0.8935 (ttp) cc_final: 0.8179 (tpt) REVERT: A 1166 ARG cc_start: 0.5320 (ttp80) cc_final: 0.2572 (tpt170) outliers start: 16 outliers final: 14 residues processed: 102 average time/residue: 0.1615 time to fit residues: 24.2143 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain A residue 274 LEU 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 824 LEU Chi-restraints excluded: chain A residue 833 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: 0.8980 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.088549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071629 restraints weight = 21315.682| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.32 r_work: 0.2955 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7704 Z= 0.130 Angle : 0.550 11.949 10601 Z= 0.266 Chirality : 0.038 0.343 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.396 13.030 1072 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.03 % Allowed : 19.05 % Favored : 78.92 % 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: 2.16 (0.29), residues: 958 helix: 2.76 (0.21), residues: 601 sheet: -0.64 (0.68), residues: 64 loop : -1.01 (0.36), residues: 293 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 0.029 0.001 TYR A 818 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 473) hydrogen bonds : angle 3.95964 ( 1374) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.57774 ( 2) covalent geometry : bond 0.00296 ( 7703) covalent geometry : angle 0.54998 (10599) ********************** 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 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 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: 0.9154 (m) cc_final: 0.8848 (p) REVERT: A 608 GLU cc_start: 0.8895 (mp0) cc_final: 0.8563 (mp0) REVERT: A 644 ARG cc_start: 0.5865 (mmt180) cc_final: 0.5351 (tpt170) REVERT: A 827 GLU cc_start: 0.9011 (tp30) cc_final: 0.8612 (tp30) REVERT: A 900 MET cc_start: 0.8960 (ttp) cc_final: 0.8177 (tpt) REVERT: A 1166 ARG cc_start: 0.5364 (ttp80) cc_final: 0.2583 (tpt170) outliers start: 15 outliers final: 14 residues processed: 96 average time/residue: 0.1615 time to fit residues: 23.1151 Evaluate side-chains 94 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 824 LEU Chi-restraints excluded: chain A residue 833 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 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.0000 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.088803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071856 restraints weight = 21038.268| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.37 r_work: 0.2963 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7704 Z= 0.120 Angle : 0.548 11.814 10601 Z= 0.266 Chirality : 0.038 0.311 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.385 13.416 1072 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % Favored : 78.78 % 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: 2.74 (0.21), residues: 601 sheet: -0.63 (0.68), residues: 64 loop : -0.99 (0.36), residues: 293 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 0.019 0.001 TYR A1168 ARG 0.003 0.000 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 473) hydrogen bonds : angle 3.95341 ( 1374) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.55828 ( 2) covalent geometry : bond 0.00271 ( 7703) covalent geometry : angle 0.54846 (10599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.40 seconds wall clock time: 64 minutes 6.30 seconds (3846.30 seconds total)