Starting phenix.real_space_refine on Mon Mar 11 11:00:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2g_27835/03_2024/8e2g_27835.pdb" } resolution = 2.99 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= -0.004 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2574 2.51 5 N 676 2.21 5 O 756 1.98 5 H 4078 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 927": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8110 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 28, 'TRANS': 494} Chain breaks: 12 Time building chain proxies: 4.26, per 1000 atoms: 0.53 Number of scatterers: 8110 At special positions: 0 Unit cell: (70.4, 78.32, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 756 8.00 N 676 7.00 C 2574 6.00 H 4078 1.00 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: 6.84 Conformation dependent library (CDL) restraints added in 847.6 milliseconds 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 24.3% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 225 through 243 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.818A pdb=" N VAL A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.612A pdb=" N MET A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 3.520A pdb=" N PHE A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.696A pdb=" N GLN A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 4.181A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.880A pdb=" N ALA A 81 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 91 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 104 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 93 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 390 removed outlier: 6.464A pdb=" N ALA A 403 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 409 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 423 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 411 " --> pdb=" O HIS A 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 419 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 513 removed outlier: 5.553A pdb=" N LEU A 505 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 574 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE A 507 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 572 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 566 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 634 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 716 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 731 through 738 removed outlier: 6.709A pdb=" N GLY A 748 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 736 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 746 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS A 744 " --> pdb=" O PRO A 738 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 902 through 903 removed outlier: 6.909A pdb=" N ILE A 914 " --> pdb=" O LEU A 923 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 940 through 945 removed outlier: 6.668A pdb=" N CYS A 955 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 943 " --> pdb=" O CYS A 953 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS A 953 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR A 945 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ARG A 951 " --> pdb=" O TYR A 945 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 414 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: 2.96 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4058 1.03 - 1.23: 22 1.23 - 1.42: 1641 1.42 - 1.62: 2432 1.62 - 1.81: 32 Bond restraints: 8185 Sorted by residual: bond pdb=" C ALA A 569 " pdb=" N GLY A 570 " ideal model delta sigma weight residual 1.331 1.319 0.012 6.60e-03 2.30e+04 3.19e+00 bond pdb=" CG1 ILE A 231 " pdb=" CD1 ILE A 231 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.31e-01 bond pdb=" CA ALA A 924 " pdb=" C ALA A 924 " ideal model delta sigma weight residual 1.529 1.521 0.008 1.04e-02 9.25e+03 5.74e-01 bond pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.24e-01 bond pdb=" N GLY A 748 " pdb=" CA GLY A 748 " ideal model delta sigma weight residual 1.456 1.447 0.008 1.16e-02 7.43e+03 4.80e-01 ... (remaining 8180 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 140 106.37 - 113.28: 9947 113.28 - 120.18: 2357 120.18 - 127.09: 2342 127.09 - 134.00: 54 Bond angle restraints: 14840 Sorted by residual: angle pdb=" N ILE A 860 " pdb=" CA ILE A 860 " pdb=" C ILE A 860 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA LEU A 861 " pdb=" CB LEU A 861 " pdb=" CG LEU A 861 " ideal model delta sigma weight residual 116.30 124.32 -8.02 3.50e+00 8.16e-02 5.25e+00 angle pdb=" CA ILE A 860 " pdb=" C ILE A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 118.65 116.61 2.04 1.07e+00 8.73e-01 3.64e+00 angle pdb=" N GLU A 343 " pdb=" CA GLU A 343 " pdb=" C GLU A 343 " ideal model delta sigma weight residual 110.14 107.38 2.76 1.51e+00 4.39e-01 3.35e+00 angle pdb=" C GLY A 570 " pdb=" N GLY A 571 " pdb=" CA GLY A 571 " ideal model delta sigma weight residual 121.58 120.04 1.54 8.60e-01 1.35e+00 3.20e+00 ... (remaining 14835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3428 17.42 - 34.84: 296 34.84 - 52.25: 99 52.25 - 69.67: 25 69.67 - 87.09: 10 Dihedral angle restraints: 3858 sinusoidal: 2118 harmonic: 1740 Sorted by residual: dihedral pdb=" CA ILE A 914 " pdb=" C ILE A 914 " pdb=" N LEU A 915 " pdb=" CA LEU A 915 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP A 430 " pdb=" CB ASP A 430 " pdb=" CG ASP A 430 " pdb=" OD1 ASP A 430 " ideal model delta sinusoidal sigma weight residual -30.00 -83.18 53.18 1 2.00e+01 2.50e-03 9.62e+00 dihedral pdb=" N LYS A 636 " pdb=" CA LYS A 636 " pdb=" CB LYS A 636 " pdb=" CG LYS A 636 " ideal model delta sinusoidal sigma weight residual -60.00 -116.64 56.64 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 342 0.027 - 0.053: 212 0.053 - 0.080: 50 0.080 - 0.106: 37 0.106 - 0.133: 24 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ILE A 512 " pdb=" N ILE A 512 " pdb=" C ILE A 512 " pdb=" CB ILE A 512 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 914 " pdb=" N ILE A 914 " pdb=" C ILE A 914 " pdb=" CB ILE A 914 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE A 944 " pdb=" N ILE A 944 " pdb=" C ILE A 944 " pdb=" CB ILE A 944 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 662 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 430 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 431 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 627 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 628 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 737 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 738 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.019 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 462 2.18 - 2.78: 16811 2.78 - 3.39: 23134 3.39 - 3.99: 30750 3.99 - 4.60: 47132 Nonbonded interactions: 118289 Sorted by model distance: nonbonded pdb=" O PRO A 929 " pdb=" H ASP A 938 " model vdw 1.572 1.850 nonbonded pdb=" OE1 GLN A 151 " pdb=" H GLN A 162 " model vdw 1.588 1.850 nonbonded pdb=" O GLU A 164 " pdb="HH22 ARG A 258 " model vdw 1.594 1.850 nonbonded pdb="HH12 ARG A 289 " pdb=" OD1 ASN A 365 " model vdw 1.598 1.850 nonbonded pdb=" H GLU A 339 " pdb=" OD2 ASP A 342 " model vdw 1.606 1.850 ... (remaining 118284 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: 8.100 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: 0.140 Extract box with map and model: 22.760 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.730 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.003 0.033 4107 Z= 0.211 Angle : 0.603 8.023 5572 Z= 0.319 Chirality : 0.043 0.133 665 Planarity : 0.005 0.042 697 Dihedral : 15.682 87.087 1489 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.42 % Allowed : 19.78 % Favored : 77.80 % 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: -1.77 (0.38), residues: 497 helix: -0.03 (0.48), residues: 120 sheet: -1.38 (0.47), residues: 135 loop : -1.59 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.013 0.002 PHE A 192 TYR 0.007 0.001 TYR A 189 ARG 0.003 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 1.7157 time to fit residues: 103.1078 Evaluate side-chains 53 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 952 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4107 Z= 0.215 Angle : 0.548 5.579 5572 Z= 0.281 Chirality : 0.043 0.150 665 Planarity : 0.004 0.044 697 Dihedral : 6.614 58.005 558 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.42 % Allowed : 18.90 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.38), residues: 497 helix: -0.22 (0.45), residues: 129 sheet: -1.28 (0.45), residues: 136 loop : -1.67 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 PHE 0.013 0.002 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 1.8036 time to fit residues: 106.1246 Evaluate side-chains 50 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4107 Z= 0.345 Angle : 0.613 5.808 5572 Z= 0.317 Chirality : 0.045 0.145 665 Planarity : 0.005 0.046 697 Dihedral : 5.914 58.772 546 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.64 % Allowed : 21.10 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.36), residues: 497 helix: -0.49 (0.44), residues: 129 sheet: -1.18 (0.48), residues: 119 loop : -1.98 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.020 0.002 PHE A 192 TYR 0.011 0.002 TYR A 315 ARG 0.002 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.618 Fit side-chains REVERT: A 853 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6172 (mp10) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 1.7230 time to fit residues: 96.3308 Evaluate side-chains 51 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4107 Z= 0.224 Angle : 0.558 5.472 5572 Z= 0.286 Chirality : 0.043 0.150 665 Planarity : 0.005 0.047 697 Dihedral : 5.698 56.630 546 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.24 % Favored : 92.56 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.37), residues: 497 helix: -0.15 (0.45), residues: 129 sheet: -1.10 (0.47), residues: 124 loop : -1.98 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.047 0.002 PHE A 920 TYR 0.007 0.001 TYR A 633 ARG 0.005 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 59 average time/residue: 1.6519 time to fit residues: 103.1217 Evaluate side-chains 53 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4107 Z= 0.283 Angle : 0.577 5.616 5572 Z= 0.296 Chirality : 0.044 0.135 665 Planarity : 0.004 0.045 697 Dihedral : 5.663 54.578 546 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.42 % Allowed : 21.32 % Favored : 76.26 % 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 (0.37), residues: 497 helix: -0.25 (0.45), residues: 129 sheet: -1.15 (0.47), residues: 124 loop : -2.08 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 345 HIS 0.004 0.001 HIS A 222 PHE 0.017 0.002 PHE A 192 TYR 0.010 0.001 TYR A 315 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 1.7837 time to fit residues: 97.7199 Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4107 Z= 0.226 Angle : 0.549 5.803 5572 Z= 0.280 Chirality : 0.043 0.145 665 Planarity : 0.004 0.046 697 Dihedral : 5.539 53.064 546 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.64 % Allowed : 20.88 % Favored : 76.48 % 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: -1.91 (0.37), residues: 497 helix: -0.10 (0.46), residues: 129 sheet: -1.11 (0.47), residues: 124 loop : -2.00 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.005 0.001 HIS A 222 PHE 0.014 0.002 PHE A 192 TYR 0.007 0.001 TYR A 315 ARG 0.003 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 1.5603 time to fit residues: 97.4765 Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4107 Z= 0.201 Angle : 0.544 6.642 5572 Z= 0.275 Chirality : 0.043 0.135 665 Planarity : 0.004 0.045 697 Dihedral : 5.407 51.798 546 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.42 % Allowed : 22.20 % Favored : 75.38 % 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: -1.93 (0.37), residues: 497 helix: -0.06 (0.45), residues: 129 sheet: -1.18 (0.48), residues: 121 loop : -2.01 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 PHE 0.013 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 1.6834 time to fit residues: 99.6771 Evaluate side-chains 53 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4107 Z= 0.220 Angle : 0.553 6.235 5572 Z= 0.279 Chirality : 0.043 0.138 665 Planarity : 0.004 0.044 697 Dihedral : 5.372 50.502 546 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.20 % Allowed : 21.76 % Favored : 76.04 % 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: -1.93 (0.37), residues: 497 helix: -0.04 (0.45), residues: 129 sheet: -1.18 (0.48), residues: 121 loop : -2.02 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 345 HIS 0.003 0.001 HIS A 222 PHE 0.014 0.002 PHE A 192 TYR 0.009 0.001 TYR A 315 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 1.8158 time to fit residues: 99.3837 Evaluate side-chains 51 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.0170 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4107 Z= 0.166 Angle : 0.531 6.128 5572 Z= 0.266 Chirality : 0.042 0.138 665 Planarity : 0.004 0.045 697 Dihedral : 5.179 49.086 546 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.54 % Allowed : 22.42 % Favored : 76.04 % 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: -1.67 (0.37), residues: 497 helix: 0.22 (0.46), residues: 129 sheet: -1.04 (0.48), residues: 121 loop : -1.88 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 296 HIS 0.003 0.001 HIS A 222 PHE 0.009 0.001 PHE A 192 TYR 0.007 0.001 TYR A 633 ARG 0.003 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6187 (pm20) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.9630 time to fit residues: 111.1716 Evaluate side-chains 50 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 4107 Z= 0.392 Angle : 0.643 7.900 5572 Z= 0.331 Chirality : 0.046 0.146 665 Planarity : 0.005 0.043 697 Dihedral : 5.614 47.300 546 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 1.32 % Allowed : 23.74 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.36), residues: 497 helix: -0.31 (0.45), residues: 129 sheet: -1.19 (0.48), residues: 120 loop : -2.15 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 345 HIS 0.005 0.001 HIS A 222 PHE 0.040 0.003 PHE A 391 TYR 0.013 0.002 TYR A 315 ARG 0.004 0.001 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 994 Ramachandran restraints generated. 497 Oldfield, 0 Emsley, 497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.6562 time to fit residues: 89.4820 Evaluate side-chains 49 residues out of total 455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.152606 restraints weight = 17173.255| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.13 r_work: 0.3881 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4107 Z= 0.202 Angle : 0.564 7.742 5572 Z= 0.284 Chirality : 0.043 0.143 665 Planarity : 0.004 0.046 697 Dihedral : 4.984 32.818 544 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.10 % Allowed : 24.40 % Favored : 74.51 % 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: -1.93 (0.37), residues: 497 helix: -0.05 (0.45), residues: 129 sheet: -1.15 (0.48), residues: 120 loop : -2.03 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.005 0.001 HIS A 222 PHE 0.032 0.002 PHE A 391 TYR 0.007 0.001 TYR A 633 ARG 0.003 0.000 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.17 seconds wall clock time: 70 minutes 33.81 seconds (4233.81 seconds total)