Starting phenix.real_space_refine on Sat Aug 3 08:21:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_44363.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_44363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_44363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_44363.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/08_2024/9b8z_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 Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.21, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.86 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: 2.52 Time building geometry restraints manager: 3.32 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: 74.62 - 95.22: 91 95.22 - 115.82: 5045 115.82 - 136.42: 5427 136.42 - 157.02: 16 157.02 - 177.62: 20 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: 2.390 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.843 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: 0.1668 time to fit residues: 33.2630 Evaluate side-chains 98 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.852 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: 0.8841 (p) REVERT: A 186 MET cc_start: 0.8932 (mmm) cc_final: 0.8630 (mmm) REVERT: A 254 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8534 (mt-10) REVERT: A 378 LEU cc_start: 0.9379 (mt) cc_final: 0.9174 (mt) REVERT: A 620 GLU cc_start: 0.8252 (tt0) cc_final: 0.8045 (tt0) REVERT: A 804 ASP cc_start: 0.7935 (t0) cc_final: 0.7602 (t0) REVERT: A 818 TYR cc_start: 0.8871 (m-10) cc_final: 0.8596 (m-80) REVERT: A 827 GLU cc_start: 0.8516 (tp30) cc_final: 0.8184 (tp30) REVERT: A 884 THR cc_start: 0.9163 (m) cc_final: 0.8742 (p) REVERT: A 900 MET cc_start: 0.8611 (ttp) cc_final: 0.8361 (tpt) REVERT: A 1166 ARG cc_start: 0.4666 (ttp80) cc_final: 0.2365 (tpt170) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.1542 time to fit residues: 25.2163 Evaluate side-chains 97 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 70 optimal weight: 0.9980 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7703 Z= 0.254 Angle : 0.521 8.048 10599 Z= 0.266 Chirality : 0.038 0.138 1193 Planarity : 0.004 0.050 1309 Dihedral : 3.493 15.856 1072 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 13.24 % Favored : 83.78 % 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: 2.36 (0.29), residues: 958 helix: 2.82 (0.21), residues: 603 sheet: -0.24 (0.68), residues: 64 loop : -0.79 (0.38), residues: 291 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 0.004 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 118 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.876 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9136 (m) cc_final: 0.8846 (p) REVERT: A 186 MET cc_start: 0.8958 (mmm) cc_final: 0.8684 (mmm) REVERT: A 804 ASP cc_start: 0.8102 (t0) cc_final: 0.7899 (t70) REVERT: A 818 TYR cc_start: 0.8949 (m-10) cc_final: 0.8690 (m-80) REVERT: A 827 GLU cc_start: 0.8516 (tp30) cc_final: 0.8242 (tp30) REVERT: A 900 MET cc_start: 0.8607 (ttp) cc_final: 0.8240 (tpt) REVERT: A 1166 ARG cc_start: 0.4772 (ttp80) cc_final: 0.2465 (tpt170) outliers start: 22 outliers final: 12 residues processed: 113 average time/residue: 0.1560 time to fit residues: 25.8358 Evaluate side-chains 100 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 87 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2101 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= 0.198 Angle : 0.497 6.601 10599 Z= 0.252 Chirality : 0.037 0.128 1193 Planarity : 0.004 0.048 1309 Dihedral : 3.481 16.593 1072 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.57 % Allowed : 14.73 % Favored : 82.70 % 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: 2.81 (0.21), residues: 602 sheet: -0.34 (0.68), residues: 65 loop : -0.84 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 PHE 0.018 0.001 PHE A 902 TYR 0.017 0.001 TYR A1168 ARG 0.002 0.000 ARG A 195 *********************** 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 118 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.838 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 9 SER cc_start: 0.8750 (m) cc_final: 0.8317 (t) REVERT: A 72 THR cc_start: 0.9144 (m) cc_final: 0.8854 (p) REVERT: A 355 MET cc_start: 0.9573 (mmp) cc_final: 0.9322 (mmm) REVERT: A 804 ASP cc_start: 0.8131 (t0) cc_final: 0.7905 (t70) REVERT: A 818 TYR cc_start: 0.8935 (m-10) cc_final: 0.8688 (m-80) REVERT: A 827 GLU cc_start: 0.8600 (tp30) cc_final: 0.8271 (tp30) REVERT: A 900 MET cc_start: 0.8577 (ttp) cc_final: 0.8227 (tpt) REVERT: A 1166 ARG cc_start: 0.4838 (ttp80) cc_final: 0.2500 (tpt170) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.1681 time to fit residues: 27.7993 Evaluate side-chains 104 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 833 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 78 optimal weight: 0.0050 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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** A1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7703 Z= 0.158 Angle : 0.513 8.210 10599 Z= 0.251 Chirality : 0.037 0.133 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.457 16.053 1072 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.84 % Allowed : 15.00 % Favored : 82.16 % 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 (0.28), residues: 958 helix: 2.82 (0.21), residues: 600 sheet: -0.17 (0.69), residues: 64 loop : -0.93 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.006 0.001 HIS A1128 PHE 0.013 0.001 PHE A 440 TYR 0.018 0.001 TYR A1168 ARG 0.002 0.000 ARG A 336 *********************** 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 117 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.772 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 9 SER cc_start: 0.8769 (m) cc_final: 0.8333 (t) REVERT: A 72 THR cc_start: 0.9125 (m) cc_final: 0.8828 (p) REVERT: A 629 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 804 ASP cc_start: 0.8132 (t0) cc_final: 0.7901 (t70) REVERT: A 818 TYR cc_start: 0.8910 (m-10) cc_final: 0.8681 (m-80) REVERT: A 827 GLU cc_start: 0.8604 (tp30) cc_final: 0.8254 (tp30) REVERT: A 884 THR cc_start: 0.9106 (m) cc_final: 0.8652 (p) REVERT: A 900 MET cc_start: 0.8542 (ttp) cc_final: 0.8209 (tpt) REVERT: A 1166 ARG cc_start: 0.4865 (ttp80) cc_final: 0.2508 (tpt170) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 0.1519 time to fit residues: 24.6042 Evaluate side-chains 101 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 833 LEU Chi-restraints excluded: chain A residue 983 MET 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 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7703 Z= 0.213 Angle : 0.533 12.208 10599 Z= 0.260 Chirality : 0.037 0.154 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.457 15.810 1072 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 15.54 % Favored : 81.62 % 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: 2.84 (0.21), residues: 600 sheet: -0.21 (0.69), residues: 64 loop : -0.96 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 PHE 0.010 0.001 PHE A 627 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 108 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 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: 0.9167 (m) cc_final: 0.8870 (p) REVERT: A 108 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8722 (mtm-85) REVERT: A 355 MET cc_start: 0.9557 (mmp) cc_final: 0.9324 (mmm) REVERT: A 644 ARG cc_start: 0.5386 (mmt180) cc_final: 0.5149 (tpt170) REVERT: A 804 ASP cc_start: 0.8151 (t0) cc_final: 0.7917 (t70) REVERT: A 818 TYR cc_start: 0.8934 (m-10) cc_final: 0.8706 (m-80) REVERT: A 827 GLU cc_start: 0.8657 (tp30) cc_final: 0.8295 (tp30) REVERT: A 900 MET cc_start: 0.8563 (ttp) cc_final: 0.8207 (tpt) REVERT: A 1166 ARG cc_start: 0.4886 (ttp80) cc_final: 0.2487 (tpt170) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.1679 time to fit residues: 25.2624 Evaluate side-chains 102 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 7.9990 chunk 53 optimal weight: 0.0000 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2531 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= 0.284 Angle : 0.553 9.390 10599 Z= 0.274 Chirality : 0.038 0.126 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.493 16.642 1072 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.70 % Allowed : 16.49 % Favored : 80.81 % 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: 2.25 (0.29), residues: 958 helix: 2.82 (0.21), residues: 600 sheet: -0.43 (0.70), residues: 64 loop : -0.99 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.006 0.001 HIS A1128 PHE 0.012 0.001 PHE A 627 TYR 0.018 0.001 TYR A1168 ARG 0.002 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 103 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 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: 0.9171 (m) cc_final: 0.8845 (p) REVERT: A 355 MET cc_start: 0.9587 (mmp) cc_final: 0.9353 (mmm) REVERT: A 644 ARG cc_start: 0.5484 (mmt180) cc_final: 0.5261 (tpt170) REVERT: A 804 ASP cc_start: 0.8197 (t0) cc_final: 0.7976 (t70) REVERT: A 818 TYR cc_start: 0.8968 (m-10) cc_final: 0.8746 (m-80) REVERT: A 827 GLU cc_start: 0.8700 (tp30) cc_final: 0.8377 (tp30) REVERT: A 900 MET cc_start: 0.8594 (ttp) cc_final: 0.8222 (tpt) REVERT: A 1166 ARG cc_start: 0.5035 (ttp80) cc_final: 0.2615 (tpt170) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.1645 time to fit residues: 23.5632 Evaluate side-chains 93 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7703 Z= 0.184 Angle : 0.524 11.130 10599 Z= 0.257 Chirality : 0.037 0.160 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.447 15.398 1072 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.57 % Allowed : 16.62 % Favored : 80.81 % 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: 600 sheet: -0.53 (0.68), residues: 64 loop : -0.99 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 403 HIS 0.006 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 287 *********************** 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 109 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.829 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: 0.8842 (p) REVERT: A 355 MET cc_start: 0.9565 (mmp) cc_final: 0.9315 (mmm) REVERT: A 644 ARG cc_start: 0.5436 (mmt180) cc_final: 0.5213 (tpt170) REVERT: A 804 ASP cc_start: 0.8174 (t0) cc_final: 0.7971 (t70) REVERT: A 827 GLU cc_start: 0.8641 (tp30) cc_final: 0.8285 (tp30) REVERT: A 900 MET cc_start: 0.8529 (ttp) cc_final: 0.8180 (tpt) REVERT: A 1166 ARG cc_start: 0.5081 (ttp80) cc_final: 0.2625 (tpt170) outliers start: 19 outliers final: 18 residues processed: 106 average time/residue: 0.1539 time to fit residues: 23.8601 Evaluate side-chains 98 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 264 VAL 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 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 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 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7703 Z= 0.239 Angle : 0.542 11.086 10599 Z= 0.268 Chirality : 0.037 0.127 1193 Planarity : 0.004 0.049 1309 Dihedral : 3.449 15.055 1072 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 600 sheet: -0.65 (0.68), residues: 64 loop : -0.97 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.011 0.001 PHE A 627 TYR 0.029 0.001 TYR A 818 ARG 0.002 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 100 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.834 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9185 (m) cc_final: 0.8867 (p) REVERT: A 186 MET cc_start: 0.9038 (mmm) cc_final: 0.8701 (mmm) REVERT: A 355 MET cc_start: 0.9571 (mmp) cc_final: 0.9336 (mmm) REVERT: A 644 ARG cc_start: 0.5512 (mmt180) cc_final: 0.5282 (tpt170) REVERT: A 827 GLU cc_start: 0.8694 (tp30) cc_final: 0.8326 (tp30) REVERT: A 900 MET cc_start: 0.8571 (ttp) cc_final: 0.8181 (tpt) REVERT: A 1166 ARG cc_start: 0.5135 (ttp80) cc_final: 0.2662 (tpt170) outliers start: 21 outliers final: 17 residues processed: 97 average time/residue: 0.1507 time to fit residues: 21.6632 Evaluate side-chains 97 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 709 THR 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 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 56 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 81 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2844 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= 0.187 Angle : 0.535 11.814 10599 Z= 0.262 Chirality : 0.037 0.182 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.428 14.353 1072 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.70 % Allowed : 17.43 % Favored : 79.86 % 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: 2.13 (0.28), residues: 958 helix: 2.73 (0.21), residues: 600 sheet: -0.67 (0.68), residues: 64 loop : -0.99 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.006 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 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 104 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.860 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9167 (m) cc_final: 0.8856 (p) REVERT: A 186 MET cc_start: 0.9010 (mmm) cc_final: 0.8643 (mmm) REVERT: A 355 MET cc_start: 0.9565 (mmp) cc_final: 0.9332 (mmm) REVERT: A 644 ARG cc_start: 0.5520 (mmt180) cc_final: 0.5272 (tpt170) REVERT: A 827 GLU cc_start: 0.8675 (tp30) cc_final: 0.8309 (tp30) REVERT: A 900 MET cc_start: 0.8530 (ttp) cc_final: 0.8138 (tpt) REVERT: A 1166 ARG cc_start: 0.5157 (ttp80) cc_final: 0.2678 (tpt170) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.1481 time to fit residues: 22.1204 Evaluate side-chains 100 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 709 THR 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 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 23 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS ** A 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.069440 restraints weight = 21177.375| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.32 r_work: 0.2888 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7703 Z= 0.362 Angle : 0.619 10.801 10599 Z= 0.307 Chirality : 0.041 0.374 1193 Planarity : 0.004 0.045 1309 Dihedral : 3.556 14.554 1072 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.43 % Allowed : 18.24 % 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: 2.10 (0.29), residues: 958 helix: 2.73 (0.22), residues: 600 sheet: -0.77 (0.68), residues: 64 loop : -1.04 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 820 HIS 0.006 0.001 HIS A1128 PHE 0.013 0.001 PHE A 627 TYR 0.019 0.002 TYR A1168 ARG 0.003 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1817.94 seconds wall clock time: 32 minutes 59.99 seconds (1979.99 seconds total)