Starting phenix.real_space_refine on Tue Jun 25 09:26:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/06_2024/9b8z_44363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/06_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_44363/06_2024/9b8z_44363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/06_2024/9b8z_44363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/06_2024/9b8z_44363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8z_44363/06_2024/9b8z_44363_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 6.02, per 1000 atoms: 0.80 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 3 sheets defined 59.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.843A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 345 through 357 removed outlier: 3.659A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 423 through 434 removed outlier: 4.489A pdb=" N ALA A 427 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 572 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 585 through 602 Processing helix chain 'A' and resid 608 through 633 Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.795A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 690 through 698 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 704 Processing helix chain 'A' and resid 767 through 777 Processing helix chain 'A' and resid 779 through 802 Processing helix chain 'A' and resid 812 through 833 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 888 through 912 removed outlier: 4.131A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 952 Proline residue: A 918 - end of helix 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 959 through 975 removed outlier: 4.825A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.926A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 1017 through 1032 Processing helix chain 'A' and resid 1034 through 1049 Processing helix chain 'A' and resid 1054 through 1071 removed outlier: 3.966A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1087 removed outlier: 4.777A pdb=" N VAL A1081 " --> pdb=" O PRO A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1141 Processing helix chain 'A' and resid 1144 through 1171 Processing sheet with id= A, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.535A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A 277 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 299 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= C, 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) 419 hydrogen bonds defined for protein. 1194 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: 2.42 Time building geometry restraints manager: 3.74 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: 6862 3.17 - 3.75: 11764 3.75 - 4.32: 15117 4.32 - 4.90: 26048 Nonbonded interactions: 59851 Sorted by model distance: nonbonded pdb=" O ARG A 353 " pdb=" OG1 THR A 356 " model vdw 2.014 2.440 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 2.520 nonbonded pdb=" N GLN A 419 " pdb=" OE1 GLN A 419 " model vdw 2.223 2.520 nonbonded pdb=" OE1 GLU A 608 " pdb=" NH1 ARG A 611 " model vdw 2.225 2.520 ... (remaining 59846 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: 2.760 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: 11.850 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 45.080 ------------------------------------------------------------------------------- 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= 0.291 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 : 0.907 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: 0.1698 time to fit residues: 33.5839 Evaluate side-chains 98 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7703 Z= 0.195 Angle : 0.498 6.404 10599 Z= 0.254 Chirality : 0.037 0.153 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.404 14.761 1072 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.03 % Allowed : 10.81 % Favored : 87.16 % 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: 2.34 (0.29), residues: 958 helix: 2.68 (0.22), residues: 605 sheet: 0.27 (0.75), residues: 59 loop : -0.65 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 680 HIS 0.007 0.001 HIS A1128 PHE 0.013 0.001 PHE A 933 TYR 0.018 0.001 TYR A1168 ARG 0.005 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 : 0.878 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9108 (m) cc_final: 0.8845 (p) REVERT: A 186 MET cc_start: 0.8924 (mmm) cc_final: 0.8562 (mmm) REVERT: A 254 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 804 ASP cc_start: 0.7917 (t0) cc_final: 0.7549 (t0) REVERT: A 818 TYR cc_start: 0.8769 (m-10) cc_final: 0.8488 (m-80) REVERT: A 827 GLU cc_start: 0.8408 (tp30) cc_final: 0.8093 (tp30) REVERT: A 884 THR cc_start: 0.9173 (m) cc_final: 0.8542 (p) REVERT: A 900 MET cc_start: 0.8602 (ttp) cc_final: 0.8365 (tpt) REVERT: A 1166 ARG cc_start: 0.4597 (ttp80) cc_final: 0.2280 (tpt170) outliers start: 15 outliers final: 8 residues processed: 112 average time/residue: 0.1618 time to fit residues: 26.0849 Evaluate side-chains 98 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 909 ILE 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: 2.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7703 Z= 0.295 Angle : 0.529 6.757 10599 Z= 0.266 Chirality : 0.038 0.132 1193 Planarity : 0.004 0.050 1309 Dihedral : 3.472 14.487 1072 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.30 % Allowed : 14.19 % Favored : 83.51 % 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: 2.59 (0.21), residues: 600 sheet: 0.23 (0.75), residues: 59 loop : -0.81 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.007 0.001 HIS A1128 PHE 0.010 0.001 PHE A 931 TYR 0.016 0.001 TYR A1168 ARG 0.006 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 117 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.896 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9182 (m) cc_final: 0.8910 (p) REVERT: A 186 MET cc_start: 0.8963 (mmm) cc_final: 0.8532 (mmp) REVERT: A 827 GLU cc_start: 0.8456 (tp30) cc_final: 0.8221 (tp30) REVERT: A 884 THR cc_start: 0.9114 (m) cc_final: 0.8425 (p) REVERT: A 900 MET cc_start: 0.8622 (ttp) cc_final: 0.8263 (tpt) REVERT: A 1166 ARG cc_start: 0.4825 (ttp80) cc_final: 0.2458 (tpt170) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.1632 time to fit residues: 26.4612 Evaluate side-chains 100 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 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 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 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: 0.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7703 Z= 0.238 Angle : 0.514 10.233 10599 Z= 0.255 Chirality : 0.037 0.127 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.475 14.448 1072 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.11 % Allowed : 13.78 % Favored : 83.11 % 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: 2.61 (0.21), residues: 594 sheet: 0.18 (0.75), residues: 59 loop : -0.80 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.006 0.001 HIS A1128 PHE 0.017 0.001 PHE A 902 TYR 0.018 0.001 TYR A1168 ARG 0.003 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.873 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: 0.8890 (p) REVERT: A 186 MET cc_start: 0.8956 (mmm) cc_final: 0.8583 (mmp) REVERT: A 355 MET cc_start: 0.9535 (mmp) cc_final: 0.9309 (mmm) REVERT: A 827 GLU cc_start: 0.8509 (tp30) cc_final: 0.8212 (tp30) REVERT: A 900 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8227 (tpt) REVERT: A 1118 GLU cc_start: 0.7621 (mp0) cc_final: 0.7404 (mp0) REVERT: A 1166 ARG cc_start: 0.4836 (ttp80) cc_final: 0.2455 (tpt170) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.1817 time to fit residues: 28.8225 Evaluate side-chains 99 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 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 900 MET Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7703 Z= 0.247 Angle : 0.513 7.824 10599 Z= 0.255 Chirality : 0.037 0.127 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.467 15.280 1072 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.11 % Allowed : 14.59 % Favored : 82.30 % 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: 2.64 (0.21), residues: 592 sheet: 0.02 (0.71), residues: 65 loop : -0.82 (0.37), residues: 301 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 902 TYR 0.018 0.001 TYR A1168 ARG 0.009 0.000 ARG A 882 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.792 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9170 (m) cc_final: 0.8888 (p) REVERT: A 186 MET cc_start: 0.8956 (mmm) cc_final: 0.8566 (mmp) REVERT: A 818 TYR cc_start: 0.8693 (m-80) cc_final: 0.8462 (m-80) REVERT: A 827 GLU cc_start: 0.8587 (tp30) cc_final: 0.8288 (tp30) REVERT: A 900 MET cc_start: 0.8576 (ttp) cc_final: 0.8230 (tpt) REVERT: A 1166 ARG cc_start: 0.4923 (ttp80) cc_final: 0.2540 (tpt170) outliers start: 23 outliers final: 13 residues processed: 114 average time/residue: 0.1706 time to fit residues: 27.4728 Evaluate side-chains 98 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 769 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 884 THR 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 31 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7703 Z= 0.216 Angle : 0.520 8.677 10599 Z= 0.254 Chirality : 0.036 0.127 1193 Planarity : 0.004 0.046 1309 Dihedral : 3.445 15.333 1072 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.84 % Allowed : 16.08 % Favored : 81.08 % 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: 2.05 (0.28), residues: 958 helix: 2.56 (0.21), residues: 596 sheet: 0.10 (0.74), residues: 59 loop : -0.92 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.006 0.001 HIS A1128 PHE 0.010 0.001 PHE A 902 TYR 0.014 0.001 TYR A1168 ARG 0.007 0.000 ARG A 882 *********************** 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 105 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.811 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9152 (m) cc_final: 0.8863 (p) REVERT: A 186 MET cc_start: 0.8923 (mmm) cc_final: 0.8572 (mmp) REVERT: A 355 MET cc_start: 0.9469 (mmp) cc_final: 0.9244 (mmm) REVERT: A 827 GLU cc_start: 0.8593 (tp30) cc_final: 0.8290 (tp30) REVERT: A 900 MET cc_start: 0.8559 (ttp) cc_final: 0.8203 (tpt) REVERT: A 1166 ARG cc_start: 0.5056 (ttp80) cc_final: 0.2636 (tpt170) outliers start: 21 outliers final: 16 residues processed: 102 average time/residue: 0.1582 time to fit residues: 23.3519 Evaluate side-chains 101 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 769 LEU Chi-restraints excluded: chain A residue 786 ASN 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 904 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1023 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: 8.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 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: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2519 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= 0.291 Angle : 0.537 6.465 10599 Z= 0.268 Chirality : 0.037 0.145 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.483 15.434 1072 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.97 % Allowed : 16.49 % Favored : 80.54 % 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: 2.04 (0.28), residues: 958 helix: 2.53 (0.22), residues: 598 sheet: -0.06 (0.69), residues: 65 loop : -0.87 (0.37), residues: 295 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 0.014 0.001 TYR A1168 ARG 0.007 0.000 ARG A 882 *********************** 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 105 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.840 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 72 THR cc_start: 0.9229 (m) cc_final: 0.8936 (p) REVERT: A 355 MET cc_start: 0.9484 (mmp) cc_final: 0.9266 (mmm) REVERT: A 644 ARG cc_start: 0.5592 (mmt180) cc_final: 0.5385 (tpt170) REVERT: A 827 GLU cc_start: 0.8651 (tp30) cc_final: 0.8341 (tp30) REVERT: A 900 MET cc_start: 0.8599 (ttp) cc_final: 0.8216 (tpt) REVERT: A 1166 ARG cc_start: 0.5107 (ttp80) cc_final: 0.2651 (tpt170) outliers start: 22 outliers final: 18 residues processed: 102 average time/residue: 0.1574 time to fit residues: 23.2521 Evaluate side-chains 101 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 648 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7703 Z= 0.154 Angle : 0.501 7.040 10599 Z= 0.248 Chirality : 0.036 0.167 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.404 15.359 1072 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 2.30 % Allowed : 17.84 % 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: 2.03 (0.28), residues: 958 helix: 2.57 (0.22), residues: 596 sheet: 0.17 (0.75), residues: 59 loop : -0.99 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 902 TYR 0.015 0.001 TYR A1168 ARG 0.006 0.000 ARG A 882 *********************** 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 111 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.843 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: 0.8830 (p) REVERT: A 355 MET cc_start: 0.9468 (mmp) cc_final: 0.9226 (mmm) REVERT: A 827 GLU cc_start: 0.8585 (tp30) cc_final: 0.8284 (tp30) REVERT: A 900 MET cc_start: 0.8523 (ttp) cc_final: 0.8128 (tpt) REVERT: A 1166 ARG cc_start: 0.5141 (ttp80) cc_final: 0.2656 (tpt170) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.1648 time to fit residues: 26.0919 Evaluate side-chains 103 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 SER 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 974 ILE Chi-restraints excluded: chain A residue 988 MET 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: 1.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 0.0470 chunk 92 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2692 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= 0.181 Angle : 0.530 12.513 10599 Z= 0.257 Chirality : 0.037 0.165 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.424 15.249 1072 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 2.16 % Allowed : 19.46 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.29), residues: 958 helix: 2.53 (0.22), residues: 596 sheet: -0.04 (0.71), residues: 66 loop : -0.96 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 680 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.014 0.001 TYR A1168 ARG 0.006 0.000 ARG A 882 *********************** 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 106 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 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: 0.9124 (m) cc_final: 0.8833 (p) REVERT: A 355 MET cc_start: 0.9478 (mmp) cc_final: 0.9249 (mmm) REVERT: A 827 GLU cc_start: 0.8501 (tp30) cc_final: 0.8234 (tp30) REVERT: A 900 MET cc_start: 0.8522 (ttp) cc_final: 0.8096 (tpt) REVERT: A 1166 ARG cc_start: 0.5191 (ttp80) cc_final: 0.2698 (tpt170) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.1595 time to fit residues: 24.0685 Evaluate side-chains 103 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 769 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 SER 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 988 MET Chi-restraints excluded: chain A residue 1023 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: 1.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2783 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= 0.192 Angle : 0.527 11.920 10599 Z= 0.256 Chirality : 0.037 0.174 1193 Planarity : 0.004 0.047 1309 Dihedral : 3.386 15.178 1072 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 2.43 % Allowed : 19.05 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.29), residues: 958 helix: 2.53 (0.22), residues: 602 sheet: -0.12 (0.70), residues: 66 loop : -1.03 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.015 0.001 TYR A1168 ARG 0.006 0.000 ARG A 882 ********************** 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 106 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.897 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. REVERT: A 72 THR cc_start: 0.9110 (m) cc_final: 0.8803 (p) REVERT: A 355 MET cc_start: 0.9480 (mmp) cc_final: 0.9251 (mmm) REVERT: A 617 PHE cc_start: 0.8585 (m-80) cc_final: 0.8293 (m-10) REVERT: A 644 ARG cc_start: 0.5461 (mmt180) cc_final: 0.5130 (tpt170) REVERT: A 827 GLU cc_start: 0.8538 (tp30) cc_final: 0.8261 (tp30) REVERT: A 900 MET cc_start: 0.8536 (ttp) cc_final: 0.8102 (tpt) REVERT: A 1166 ARG cc_start: 0.5194 (ttp80) cc_final: 0.2703 (tpt170) outliers start: 18 outliers final: 17 residues processed: 104 average time/residue: 0.1668 time to fit residues: 25.1776 Evaluate side-chains 104 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 769 LEU Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 798 SER 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 988 MET 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: 1.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071160 restraints weight = 21243.351| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.32 r_work: 0.2943 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 7703 Z= 0.253 Angle : 0.904 59.197 10599 Z= 0.547 Chirality : 0.040 0.512 1193 Planarity : 0.004 0.063 1309 Dihedral : 3.541 33.934 1072 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.24 % Favored : 96.56 % Rotamer: Outliers : 2.16 % Allowed : 19.19 % Favored : 78.65 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.28), residues: 958 helix: 2.46 (0.22), residues: 602 sheet: -0.11 (0.70), residues: 66 loop : -1.03 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1124 HIS 0.005 0.001 HIS A1128 PHE 0.009 0.001 PHE A 627 TYR 0.014 0.001 TYR A1168 ARG 0.006 0.000 ARG A 882 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.93 seconds wall clock time: 33 minutes 52.63 seconds (2032.63 seconds total)