Starting phenix.real_space_refine on Sun Mar 10 22:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1y_14243/03_2024/7r1y_14243.pdb" } resolution = 3.0 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= 0.001 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3615 2.51 5 N 982 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5704 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 689} Chain breaks: 11 Time building chain proxies: 3.49, per 1000 atoms: 0.61 Number of scatterers: 5704 At special positions: 0 Unit cell: (71.9488, 74.752, 122.406, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1074 8.00 N 982 7.00 C 3615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 43.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 removed outlier: 3.679A pdb=" N ARG A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.633A pdb=" N GLN A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.522A pdb=" N VAL A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 326 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.781A pdb=" N SER A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 689 through 710 Processing helix chain 'A' and resid 761 through 787 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 797 through 806 removed outlier: 3.605A pdb=" N ILE A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.534A pdb=" N ASP A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 875 through 892 removed outlier: 3.620A pdb=" N LYS A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 880 " --> pdb=" O LYS A 876 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 881 " --> pdb=" O THR A 877 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.516A pdb=" N VAL A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 927 removed outlier: 3.589A pdb=" N ASP A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.552A pdb=" N CYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.797A pdb=" N TYR A 355 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 376 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 353 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.546A pdb=" N ALA A 446 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.584A pdb=" N GLY A 107 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 220 removed outlier: 6.627A pdb=" N ALA A 229 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 218 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A 227 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 226 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 271 removed outlier: 3.694A pdb=" N GLN A 267 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 287 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 286 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 303 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 288 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 400 removed outlier: 3.707A pdb=" N ARG A 396 " --> pdb=" O ALA A 407 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1156 1.46 - 1.58: 2701 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 5801 Sorted by residual: bond pdb=" C PRO A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.23e+00 bond pdb=" C VAL A 897 " pdb=" N ASP A 898 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.30e-02 5.92e+03 9.08e-01 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.529 1.520 0.009 1.04e-02 9.25e+03 7.29e-01 bond pdb=" C ALA A 229 " pdb=" N GLY A 230 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.71e-01 bond pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 1.517 1.524 -0.007 9.30e-03 1.16e+04 6.23e-01 ... (remaining 5796 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.77: 175 106.77 - 113.56: 3243 113.56 - 120.35: 2031 120.35 - 127.14: 2344 127.14 - 133.93: 59 Bond angle restraints: 7852 Sorted by residual: angle pdb=" N ILE A 893 " pdb=" CA ILE A 893 " pdb=" C ILE A 893 " ideal model delta sigma weight residual 113.20 109.80 3.40 9.60e-01 1.09e+00 1.25e+01 angle pdb=" C VAL A 897 " pdb=" N ASP A 898 " pdb=" CA ASP A 898 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta sigma weight residual 122.93 119.05 3.88 1.21e+00 6.83e-01 1.03e+01 angle pdb=" N ASP A 898 " pdb=" CA ASP A 898 " pdb=" C ASP A 898 " ideal model delta sigma weight residual 111.17 115.52 -4.35 1.41e+00 5.03e-01 9.51e+00 angle pdb=" N PRO A 110 " pdb=" CA PRO A 110 " pdb=" C PRO A 110 " ideal model delta sigma weight residual 110.70 114.00 -3.30 1.22e+00 6.72e-01 7.33e+00 ... (remaining 7847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3267 17.24 - 34.47: 189 34.47 - 51.71: 80 51.71 - 68.94: 8 68.94 - 86.18: 4 Dihedral angle restraints: 3548 sinusoidal: 1438 harmonic: 2110 Sorted by residual: dihedral pdb=" CA HIS A 349 " pdb=" C HIS A 349 " pdb=" N ALA A 350 " pdb=" CA ALA A 350 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PRO A 468 " pdb=" C PRO A 468 " pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ILE A 469 " pdb=" C ILE A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 539 0.027 - 0.054: 225 0.054 - 0.081: 86 0.081 - 0.108: 37 0.108 - 0.135: 24 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 416 " pdb=" N ILE A 416 " pdb=" C ILE A 416 " pdb=" CB ILE A 416 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 908 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 52 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 110 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 111 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 473 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.022 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1103 2.78 - 3.31: 5462 3.31 - 3.84: 9467 3.84 - 4.37: 11138 4.37 - 4.90: 19024 Nonbonded interactions: 46194 Sorted by model distance: nonbonded pdb=" N LEU A 145 " pdb=" O ALA A 168 " model vdw 2.252 2.520 nonbonded pdb=" OG1 THR A 169 " pdb=" O ASP A 172 " model vdw 2.302 2.440 nonbonded pdb=" OE1 GLN A 287 " pdb=" OH TYR A 289 " model vdw 2.334 2.440 nonbonded pdb=" OE1 GLN A 891 " pdb=" OG1 THR A 921 " model vdw 2.353 2.440 nonbonded pdb=" OD2 ASP A 232 " pdb=" OH TYR A 236 " model vdw 2.361 2.440 ... (remaining 46189 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: 0.390 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: 0.010 Extract box with map and model: 1.950 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.560 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.002 0.039 5801 Z= 0.157 Angle : 0.524 8.992 7852 Z= 0.293 Chirality : 0.041 0.135 911 Planarity : 0.004 0.046 1008 Dihedral : 13.126 86.178 2170 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.44 % Allowed : 11.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 699 helix: 1.36 (0.31), residues: 286 sheet: -0.03 (0.42), residues: 156 loop : -0.79 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.014 0.001 PHE A 497 TYR 0.007 0.001 TYR A 206 ARG 0.003 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.684 Fit side-chains REVERT: A 157 PHE cc_start: 0.3986 (OUTLIER) cc_final: 0.3626 (t80) REVERT: A 806 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7312 (tt) REVERT: A 855 THR cc_start: 0.7815 (p) cc_final: 0.7476 (t) REVERT: A 962 THR cc_start: 0.6266 (m) cc_final: 0.5905 (p) outliers start: 22 outliers final: 8 residues processed: 128 average time/residue: 0.9527 time to fit residues: 129.0136 Evaluate side-chains 71 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 891 GLN ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5801 Z= 0.263 Angle : 0.617 9.714 7852 Z= 0.319 Chirality : 0.043 0.165 911 Planarity : 0.005 0.039 1008 Dihedral : 6.621 55.371 787 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.73 % Allowed : 15.81 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.32), residues: 699 helix: 1.72 (0.31), residues: 282 sheet: -0.07 (0.42), residues: 148 loop : -0.70 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.005 0.001 HIS A 498 PHE 0.012 0.002 PHE A 497 TYR 0.012 0.002 TYR A 128 ARG 0.003 0.001 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 71 time to evaluate : 0.690 Fit side-chains REVERT: A 157 PHE cc_start: 0.3939 (OUTLIER) cc_final: 0.3440 (t80) REVERT: A 691 GLN cc_start: 0.7109 (tp40) cc_final: 0.6775 (tp40) REVERT: A 780 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6373 (tt) REVERT: A 806 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7390 (tt) REVERT: A 855 THR cc_start: 0.7817 (p) cc_final: 0.7518 (t) REVERT: A 911 PHE cc_start: 0.7088 (t80) cc_final: 0.6831 (t80) REVERT: A 962 THR cc_start: 0.6571 (m) cc_final: 0.6218 (p) outliers start: 43 outliers final: 17 residues processed: 105 average time/residue: 0.8327 time to fit residues: 93.1910 Evaluate side-chains 82 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5801 Z= 0.179 Angle : 0.552 8.205 7852 Z= 0.282 Chirality : 0.042 0.230 911 Planarity : 0.004 0.040 1008 Dihedral : 6.064 53.113 785 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 8.14 % Allowed : 15.34 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 699 helix: 1.88 (0.31), residues: 285 sheet: 0.06 (0.42), residues: 148 loop : -0.75 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 497 TYR 0.018 0.001 TYR A 775 ARG 0.002 0.000 ARG A 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 63 time to evaluate : 0.692 Fit side-chains REVERT: A 136 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.4539 (p90) REVERT: A 151 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7806 (ttmm) REVERT: A 157 PHE cc_start: 0.3963 (OUTLIER) cc_final: 0.3584 (t80) REVERT: A 330 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: A 780 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6363 (tt) REVERT: A 806 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7341 (tt) REVERT: A 855 THR cc_start: 0.7807 (p) cc_final: 0.7505 (t) REVERT: A 912 TYR cc_start: 0.4968 (OUTLIER) cc_final: 0.4369 (p90) REVERT: A 962 THR cc_start: 0.6284 (m) cc_final: 0.5988 (p) outliers start: 52 outliers final: 16 residues processed: 102 average time/residue: 0.8650 time to fit residues: 93.9079 Evaluate side-chains 78 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 905 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5801 Z= 0.197 Angle : 0.581 12.175 7852 Z= 0.290 Chirality : 0.042 0.143 911 Planarity : 0.004 0.038 1008 Dihedral : 5.758 53.877 782 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.73 % Allowed : 18.47 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.32), residues: 699 helix: 1.88 (0.31), residues: 286 sheet: 0.04 (0.42), residues: 148 loop : -0.69 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.020 0.002 TYR A 775 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 61 time to evaluate : 0.691 Fit side-chains REVERT: A 136 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4550 (p90) REVERT: A 330 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: A 341 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.6065 (m-30) REVERT: A 691 GLN cc_start: 0.7168 (tp40) cc_final: 0.6802 (tp40) REVERT: A 780 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6339 (tt) REVERT: A 806 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7329 (tt) REVERT: A 855 THR cc_start: 0.7831 (p) cc_final: 0.7524 (t) REVERT: A 895 ASN cc_start: 0.6446 (OUTLIER) cc_final: 0.5938 (m-40) REVERT: A 912 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.4499 (p90) REVERT: A 962 THR cc_start: 0.6318 (m) cc_final: 0.6026 (p) outliers start: 43 outliers final: 21 residues processed: 93 average time/residue: 0.8736 time to fit residues: 86.6112 Evaluate side-chains 83 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 55 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 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 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5801 Z= 0.185 Angle : 0.543 7.669 7852 Z= 0.278 Chirality : 0.041 0.140 911 Planarity : 0.004 0.039 1008 Dihedral : 5.611 54.184 780 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 7.51 % Allowed : 18.94 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.32), residues: 699 helix: 2.04 (0.31), residues: 286 sheet: 0.01 (0.42), residues: 151 loop : -0.65 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.018 0.001 TYR A 775 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 62 time to evaluate : 0.702 Fit side-chains REVERT: A 114 ARG cc_start: 0.5878 (tpp80) cc_final: 0.3978 (mtm180) REVERT: A 136 TYR cc_start: 0.4992 (OUTLIER) cc_final: 0.4574 (p90) REVERT: A 321 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 330 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: A 341 ASP cc_start: 0.6285 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: A 691 GLN cc_start: 0.7026 (tp40) cc_final: 0.6699 (tp40) REVERT: A 775 TYR cc_start: 0.7467 (t80) cc_final: 0.7224 (t80) REVERT: A 780 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6315 (tt) REVERT: A 806 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7308 (tt) REVERT: A 855 THR cc_start: 0.7836 (p) cc_final: 0.7560 (t) REVERT: A 895 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.5911 (m-40) REVERT: A 962 THR cc_start: 0.6241 (m) cc_final: 0.5961 (p) outliers start: 48 outliers final: 20 residues processed: 99 average time/residue: 0.8626 time to fit residues: 91.1388 Evaluate side-chains 85 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 58 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5801 Z= 0.173 Angle : 0.551 11.697 7852 Z= 0.279 Chirality : 0.042 0.326 911 Planarity : 0.004 0.039 1008 Dihedral : 5.523 53.943 780 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.89 % Allowed : 20.19 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 699 helix: 2.07 (0.31), residues: 286 sheet: 0.01 (0.42), residues: 151 loop : -0.62 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.016 0.001 TYR A 775 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 64 time to evaluate : 0.664 Fit side-chains REVERT: A 63 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7327 (mmp) REVERT: A 114 ARG cc_start: 0.5786 (tpp80) cc_final: 0.3946 (mtm180) REVERT: A 120 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6345 (t0) REVERT: A 136 TYR cc_start: 0.4977 (OUTLIER) cc_final: 0.4551 (p90) REVERT: A 321 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 330 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: A 780 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6329 (tt) REVERT: A 806 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7253 (tt) REVERT: A 855 THR cc_start: 0.7837 (p) cc_final: 0.7503 (t) REVERT: A 895 ASN cc_start: 0.6387 (OUTLIER) cc_final: 0.5847 (m-40) REVERT: A 962 THR cc_start: 0.6232 (m) cc_final: 0.5957 (p) REVERT: A 966 GLN cc_start: 0.6942 (mt0) cc_final: 0.6469 (mm-40) outliers start: 44 outliers final: 19 residues processed: 96 average time/residue: 0.8434 time to fit residues: 86.4048 Evaluate side-chains 85 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 58 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5801 Z= 0.182 Angle : 0.555 7.660 7852 Z= 0.281 Chirality : 0.041 0.139 911 Planarity : 0.004 0.039 1008 Dihedral : 5.540 54.197 780 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.57 % Allowed : 20.50 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.32), residues: 699 helix: 2.00 (0.31), residues: 286 sheet: 0.02 (0.42), residues: 151 loop : -0.59 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 116 HIS 0.004 0.001 HIS A 498 PHE 0.010 0.001 PHE A 497 TYR 0.016 0.001 TYR A 775 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 63 time to evaluate : 0.692 Fit side-chains REVERT: A 63 MET cc_start: 0.7605 (mmp) cc_final: 0.7351 (mmp) REVERT: A 114 ARG cc_start: 0.5824 (tpp80) cc_final: 0.3976 (mtm180) REVERT: A 120 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6290 (t0) REVERT: A 136 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.4501 (p90) REVERT: A 321 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6564 (p0) REVERT: A 330 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: A 691 GLN cc_start: 0.7198 (tp40) cc_final: 0.6941 (tp40) REVERT: A 692 LEU cc_start: 0.7821 (tp) cc_final: 0.7604 (tp) REVERT: A 780 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6050 (tt) REVERT: A 806 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7252 (tt) REVERT: A 855 THR cc_start: 0.7849 (p) cc_final: 0.7530 (t) REVERT: A 895 ASN cc_start: 0.6519 (OUTLIER) cc_final: 0.5957 (m-40) REVERT: A 962 THR cc_start: 0.6240 (m) cc_final: 0.5946 (p) REVERT: A 966 GLN cc_start: 0.6903 (mt0) cc_final: 0.6446 (mm-40) outliers start: 42 outliers final: 22 residues processed: 95 average time/residue: 0.8593 time to fit residues: 87.0000 Evaluate side-chains 86 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 57 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5801 Z= 0.163 Angle : 0.547 9.374 7852 Z= 0.280 Chirality : 0.042 0.209 911 Planarity : 0.004 0.040 1008 Dihedral : 5.399 53.573 780 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.48 % Allowed : 21.60 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.32), residues: 699 helix: 1.99 (0.31), residues: 286 sheet: 0.05 (0.41), residues: 153 loop : -0.55 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.016 0.001 TYR A 775 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 59 time to evaluate : 0.588 Fit side-chains REVERT: A 63 MET cc_start: 0.7611 (mmp) cc_final: 0.7356 (mmp) REVERT: A 114 ARG cc_start: 0.5553 (tpp80) cc_final: 0.3772 (mtm180) REVERT: A 136 TYR cc_start: 0.5068 (OUTLIER) cc_final: 0.4699 (p90) REVERT: A 321 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6532 (p0) REVERT: A 691 GLN cc_start: 0.7038 (tp40) cc_final: 0.6807 (tp40) REVERT: A 692 LEU cc_start: 0.7824 (tp) cc_final: 0.7600 (tp) REVERT: A 701 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6557 (mtpp) REVERT: A 771 VAL cc_start: 0.7473 (p) cc_final: 0.7268 (t) REVERT: A 780 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6054 (tt) REVERT: A 806 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7193 (tt) REVERT: A 855 THR cc_start: 0.7758 (p) cc_final: 0.7449 (t) REVERT: A 895 ASN cc_start: 0.6400 (OUTLIER) cc_final: 0.5837 (m-40) REVERT: A 962 THR cc_start: 0.6215 (m) cc_final: 0.5921 (p) REVERT: A 966 GLN cc_start: 0.6886 (mt0) cc_final: 0.6441 (mm-40) outliers start: 35 outliers final: 19 residues processed: 86 average time/residue: 0.9635 time to fit residues: 87.9228 Evaluate side-chains 82 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 701 LYS Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Chi-restraints excluded: chain A residue 912 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5801 Z= 0.221 Angle : 0.587 9.946 7852 Z= 0.300 Chirality : 0.043 0.228 911 Planarity : 0.004 0.038 1008 Dihedral : 5.309 49.973 778 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.32 % Allowed : 21.91 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 699 helix: 1.83 (0.31), residues: 286 sheet: 0.01 (0.42), residues: 151 loop : -0.60 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 116 HIS 0.005 0.001 HIS A 498 PHE 0.010 0.001 PHE A 497 TYR 0.025 0.002 TYR A 775 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 59 time to evaluate : 0.739 Fit side-chains REVERT: A 125 MET cc_start: 0.7406 (mtt) cc_final: 0.7140 (mtp) REVERT: A 136 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.4602 (p90) REVERT: A 321 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6575 (p0) REVERT: A 412 GLU cc_start: 0.5939 (tp30) cc_final: 0.5673 (mm-30) REVERT: A 691 GLN cc_start: 0.7086 (tp40) cc_final: 0.6838 (tp40) REVERT: A 771 VAL cc_start: 0.7491 (p) cc_final: 0.7290 (t) REVERT: A 780 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6216 (tt) REVERT: A 806 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7274 (tt) REVERT: A 855 THR cc_start: 0.7774 (p) cc_final: 0.7488 (t) REVERT: A 895 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.6034 (m-40) REVERT: A 962 THR cc_start: 0.6295 (m) cc_final: 0.5981 (p) REVERT: A 966 GLN cc_start: 0.6909 (mt0) cc_final: 0.6456 (mm-40) outliers start: 34 outliers final: 20 residues processed: 85 average time/residue: 0.8765 time to fit residues: 79.3024 Evaluate side-chains 83 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 58 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 17 optimal weight: 3.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5801 Z= 0.153 Angle : 0.555 10.717 7852 Z= 0.281 Chirality : 0.042 0.248 911 Planarity : 0.004 0.041 1008 Dihedral : 5.007 46.313 778 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.91 % Allowed : 23.63 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.32), residues: 699 helix: 2.00 (0.31), residues: 287 sheet: 0.07 (0.42), residues: 153 loop : -0.44 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 418 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.028 0.001 TYR A 775 ARG 0.002 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.705 Fit side-chains REVERT: A 125 MET cc_start: 0.7201 (mtt) cc_final: 0.6975 (mtp) REVERT: A 412 GLU cc_start: 0.5847 (tp30) cc_final: 0.5632 (mm-30) REVERT: A 771 VAL cc_start: 0.7407 (p) cc_final: 0.7195 (t) REVERT: A 780 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6058 (tt) REVERT: A 806 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 855 THR cc_start: 0.7673 (p) cc_final: 0.7392 (t) REVERT: A 884 ARG cc_start: 0.7754 (mpt-90) cc_final: 0.7523 (mpt-90) REVERT: A 962 THR cc_start: 0.6195 (m) cc_final: 0.5896 (p) REVERT: A 966 GLN cc_start: 0.6809 (mt0) cc_final: 0.6404 (mm-40) outliers start: 25 outliers final: 17 residues processed: 81 average time/residue: 0.9371 time to fit residues: 80.7434 Evaluate side-chains 77 residues out of total 639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 906 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.0070 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.174583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153440 restraints weight = 9014.090| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.92 r_work: 0.3924 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.002 0.035 5801 Z= 0.151 Angle : 0.554 10.229 7852 Z= 0.280 Chirality : 0.042 0.239 911 Planarity : 0.004 0.040 1008 Dihedral : 4.552 44.263 776 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.44 % Allowed : 24.26 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.14 (0.32), residues: 699 helix: 2.08 (0.31), residues: 288 sheet: 0.23 (0.42), residues: 153 loop : -0.39 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 418 HIS 0.003 0.001 HIS A 498 PHE 0.011 0.001 PHE A 497 TYR 0.029 0.001 TYR A 775 ARG 0.005 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.30 seconds wall clock time: 40 minutes 56.61 seconds (2456.61 seconds total)