Starting phenix.real_space_refine on Mon Mar 11 08:54:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy4_29552/03_2024/8fy4_29552.pdb" } resolution = 2.57 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= 0.001 sd= 0.018 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 40 5.16 5 C 5016 2.51 5 N 1332 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 4326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4326 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 7 Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.48, per 1000 atoms: 0.57 Number of scatterers: 7800 At special positions: 0 Unit cell: (70.854, 80.976, 151.107, 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 40 16.00 O 1412 8.00 N 1332 7.00 C 5016 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: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 74.3% alpha, 0.2% 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 4 through 19 Processing helix chain 'A' and resid 24 through 54 Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 67 through 82 removed outlier: 4.191A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.687A pdb=" N ASN A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.960A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 162 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.670A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.282A pdb=" N LEU A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 40 removed outlier: 3.883A pdb=" N LEU B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 56 Processing helix chain 'B' and resid 59 through 74 removed outlier: 4.251A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.509A pdb=" N TYR B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.949A pdb=" N PHE B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 163 through 180 Processing helix chain 'B' and resid 205 through 230 removed outlier: 3.606A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 4.375A pdb=" N ARG B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 329 removed outlier: 3.566A pdb=" N PHE B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.935A pdb=" N LYS B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.528A pdb=" N LEU B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 388 through 403 Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.757A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.776A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.851A pdb=" N ILE B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.786A pdb=" N GLN B 701 " --> pdb=" O GLN B 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.581A pdb=" N SER C 47 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.753A pdb=" N VAL C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.603A pdb=" N ARG C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.986A pdb=" N PHE C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.693A pdb=" N PHE C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 4.032A pdb=" N ILE C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.847A pdb=" N GLU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 224 through 233 Processing sheet with id=AA1, first strand: chain 'C' and resid 203 through 204 494 hydrogen bonds defined for protein. 1443 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: 2.20 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2516 1.34 - 1.46: 1455 1.46 - 1.58: 3929 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 7957 Sorted by residual: bond pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB GLN B 137 " pdb=" CG GLN B 137 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB ASP A 237 " pdb=" CG ASP A 237 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 7952 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.83: 206 105.83 - 112.88: 4321 112.88 - 119.93: 2625 119.93 - 126.98: 3515 126.98 - 134.04: 92 Bond angle restraints: 10759 Sorted by residual: angle pdb=" CB MET C 170 " pdb=" CG MET C 170 " pdb=" SD MET C 170 " ideal model delta sigma weight residual 112.70 125.65 -12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CA LYS B 176 " pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 128.27 -11.97 3.50e+00 8.16e-02 1.17e+01 angle pdb=" CB LYS C 31 " pdb=" CG LYS C 31 " pdb=" CD LYS C 31 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CB LYS B 176 " pdb=" CG LYS B 176 " pdb=" CD LYS B 176 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.90e+00 ... (remaining 10754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4345 17.75 - 35.50: 391 35.50 - 53.26: 100 53.26 - 71.01: 21 71.01 - 88.76: 4 Dihedral angle restraints: 4861 sinusoidal: 1959 harmonic: 2902 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" CB ASP C 209 " pdb=" CG ASP C 209 " pdb=" OD1 ASP C 209 " ideal model delta sinusoidal sigma weight residual -30.00 -86.66 56.66 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP C 259 " pdb=" CB ASP C 259 " pdb=" CG ASP C 259 " pdb=" OD1 ASP C 259 " ideal model delta sinusoidal sigma weight residual -30.00 -85.21 55.21 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " pdb=" CE MET B 285 " ideal model delta sinusoidal sigma weight residual 180.00 120.92 59.08 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 809 0.027 - 0.054: 263 0.054 - 0.081: 101 0.081 - 0.108: 45 0.108 - 0.136: 13 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA ILE B 424 " pdb=" N ILE B 424 " pdb=" C ILE B 424 " pdb=" CB ILE B 424 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CB ILE C 181 " pdb=" CA ILE C 181 " pdb=" CG1 ILE C 181 " pdb=" CG2 ILE C 181 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1228 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 141 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 142 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CD GLU C 64 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 163 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 164 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.020 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 387 2.73 - 3.27: 8194 3.27 - 3.82: 13833 3.82 - 4.36: 15628 4.36 - 4.90: 27191 Nonbonded interactions: 65233 Sorted by model distance: nonbonded pdb=" N GLN C 226 " pdb=" OE1 GLN C 226 " model vdw 2.189 2.520 nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 163 " model vdw 2.206 2.440 nonbonded pdb=" O PHE A 214 " pdb=" OH TYR A 228 " model vdw 2.217 2.440 nonbonded pdb=" N GLN C 274 " pdb=" OE1 GLN C 274 " model vdw 2.218 2.520 nonbonded pdb=" N GLU A 179 " pdb=" OE1 GLU A 179 " model vdw 2.229 2.520 ... (remaining 65228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.430 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 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 0.043 7957 Z= 0.178 Angle : 0.570 12.948 10759 Z= 0.280 Chirality : 0.036 0.136 1231 Planarity : 0.004 0.043 1371 Dihedral : 14.867 88.761 2965 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.87 % Allowed : 18.55 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 2.42 (0.28), residues: 957 helix: 2.16 (0.21), residues: 681 sheet: None (None), residues: 0 loop : 0.27 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 275 HIS 0.003 0.001 HIS B 430 PHE 0.009 0.001 PHE B 284 TYR 0.017 0.001 TYR B 136 ARG 0.004 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.932 Fit side-chains REVERT: A 31 GLU cc_start: 0.6566 (tt0) cc_final: 0.6320 (tt0) REVERT: A 67 ASP cc_start: 0.7051 (p0) cc_final: 0.6842 (p0) REVERT: A 138 SER cc_start: 0.7279 (m) cc_final: 0.6682 (p) REVERT: B 243 MET cc_start: 0.0653 (mmt) cc_final: 0.0161 (mmt) REVERT: B 285 MET cc_start: 0.3848 (mmp) cc_final: 0.2687 (mmp) REVERT: B 459 GLU cc_start: 0.6679 (mp0) cc_final: 0.6115 (mp0) REVERT: B 530 ASN cc_start: 0.5968 (t0) cc_final: 0.5729 (t0) REVERT: B 548 ASP cc_start: 0.6645 (t0) cc_final: 0.6314 (t0) REVERT: B 549 ASN cc_start: 0.7057 (m-40) cc_final: 0.6553 (p0) REVERT: B 551 MET cc_start: 0.7028 (mmm) cc_final: 0.6682 (mmp) REVERT: B 561 GLN cc_start: 0.7167 (mt0) cc_final: 0.6544 (mp10) REVERT: B 582 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6711 (mt) REVERT: B 664 LYS cc_start: 0.6414 (ttmm) cc_final: 0.6190 (ttmt) REVERT: C 182 SER cc_start: 0.6862 (t) cc_final: 0.6594 (m) REVERT: C 190 GLU cc_start: 0.6851 (tp30) cc_final: 0.6497 (tp30) outliers start: 16 outliers final: 8 residues processed: 138 average time/residue: 1.2527 time to fit residues: 183.2588 Evaluate side-chains 116 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 243 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 135 ASN A 151 GLN A 200 GLN A 216 GLN B 88 GLN B 163 GLN B 169 HIS ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 364 GLN B 383 GLN B 561 GLN B 632 GLN B 695 ASN C 58 HIS C 192 GLN C 271 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7957 Z= 0.366 Angle : 0.731 10.068 10759 Z= 0.366 Chirality : 0.044 0.283 1231 Planarity : 0.005 0.055 1371 Dihedral : 5.316 48.853 1060 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.90 % Allowed : 16.80 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.59 (0.27), residues: 957 helix: 1.51 (0.20), residues: 697 sheet: None (None), residues: 0 loop : -0.03 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 296 HIS 0.014 0.002 HIS B 303 PHE 0.022 0.003 PHE B 295 TYR 0.017 0.002 TYR B 429 ARG 0.005 0.001 ARG B 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.7060 (tp-100) cc_final: 0.6852 (tp-100) REVERT: A 38 ARG cc_start: 0.6391 (tpt90) cc_final: 0.6138 (tpt90) REVERT: A 114 GLN cc_start: 0.6903 (mt0) cc_final: 0.6560 (mm110) REVERT: B 176 LYS cc_start: 0.5817 (tmmt) cc_final: 0.5560 (tmmt) REVERT: B 243 MET cc_start: 0.0896 (mmt) cc_final: 0.0494 (mmt) REVERT: B 265 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6876 (p0) REVERT: B 285 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4653 (mmp) REVERT: B 317 LYS cc_start: 0.6566 (mtmp) cc_final: 0.6249 (mtmp) REVERT: B 321 GLN cc_start: 0.6602 (pt0) cc_final: 0.6324 (pt0) REVERT: B 397 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7180 (mt-10) REVERT: B 459 GLU cc_start: 0.7114 (mp0) cc_final: 0.6495 (mp0) REVERT: B 530 ASN cc_start: 0.6232 (t0) cc_final: 0.5802 (t0) REVERT: B 534 SER cc_start: 0.7769 (t) cc_final: 0.7532 (m) REVERT: B 561 GLN cc_start: 0.7268 (mt0) cc_final: 0.6653 (mp10) REVERT: B 579 GLU cc_start: 0.7181 (tt0) cc_final: 0.6916 (tt0) REVERT: B 698 LEU cc_start: 0.6473 (tt) cc_final: 0.6236 (tm) outliers start: 42 outliers final: 13 residues processed: 175 average time/residue: 1.2806 time to fit residues: 236.4969 Evaluate side-chains 141 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 125 GLN B 108 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN C 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7957 Z= 0.334 Angle : 0.621 8.884 10759 Z= 0.309 Chirality : 0.041 0.163 1231 Planarity : 0.005 0.042 1371 Dihedral : 4.892 44.333 1053 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.78 % Allowed : 19.49 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.62 (0.27), residues: 957 helix: 1.53 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 275 HIS 0.008 0.001 HIS C 58 PHE 0.022 0.002 PHE C 247 TYR 0.022 0.002 TYR B 355 ARG 0.007 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7526 (tt0) cc_final: 0.7260 (tt0) REVERT: A 76 GLN cc_start: 0.6801 (tt0) cc_final: 0.6303 (tt0) REVERT: A 114 GLN cc_start: 0.6856 (mt0) cc_final: 0.6622 (mm-40) REVERT: A 216 GLN cc_start: 0.6919 (mt0) cc_final: 0.6638 (mt0) REVERT: B 127 GLU cc_start: 0.6196 (mp0) cc_final: 0.5991 (mp0) REVERT: B 143 GLU cc_start: 0.5788 (tm-30) cc_final: 0.5481 (tm-30) REVERT: B 176 LYS cc_start: 0.5994 (tmmt) cc_final: 0.5744 (tmmt) REVERT: B 243 MET cc_start: 0.1681 (mmt) cc_final: 0.1466 (mmt) REVERT: B 267 ARG cc_start: 0.7054 (mmt180) cc_final: 0.6812 (mmt-90) REVERT: B 380 GLU cc_start: 0.6631 (tp30) cc_final: 0.5995 (mm-30) REVERT: B 397 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7240 (mt-10) REVERT: B 525 LYS cc_start: 0.6756 (tptt) cc_final: 0.6447 (tptt) REVERT: B 561 GLN cc_start: 0.7340 (mt0) cc_final: 0.6574 (mp10) REVERT: B 569 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7232 (mp) REVERT: B 668 GLN cc_start: 0.7002 (tt0) cc_final: 0.6790 (tt0) REVERT: B 690 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6665 (mm-30) REVERT: B 698 LEU cc_start: 0.6644 (tt) cc_final: 0.6426 (tt) REVERT: C 64 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6736 (pp20) REVERT: C 68 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7637 (tp) REVERT: C 150 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5753 (pp30) REVERT: C 229 GLU cc_start: 0.6992 (tt0) cc_final: 0.6745 (tt0) outliers start: 41 outliers final: 13 residues processed: 188 average time/residue: 1.2536 time to fit residues: 248.5519 Evaluate side-chains 169 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 150 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 81 ASN B 108 ASN B 265 ASN B 526 GLN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7957 Z= 0.276 Angle : 0.570 8.922 10759 Z= 0.281 Chirality : 0.039 0.157 1231 Planarity : 0.005 0.054 1371 Dihedral : 4.656 46.411 1050 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.32 % Allowed : 20.77 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.70 (0.27), residues: 957 helix: 1.59 (0.20), residues: 693 sheet: None (None), residues: 0 loop : 0.03 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.005 0.001 HIS B 303 PHE 0.021 0.002 PHE C 247 TYR 0.019 0.001 TYR B 355 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.6766 (tt0) cc_final: 0.6330 (tt0) REVERT: A 114 GLN cc_start: 0.6794 (mt0) cc_final: 0.6583 (mm-40) REVERT: A 216 GLN cc_start: 0.6936 (mt0) cc_final: 0.6689 (mt0) REVERT: B 88 GLN cc_start: 0.6867 (tt0) cc_final: 0.6633 (tt0) REVERT: B 127 GLU cc_start: 0.6296 (mp0) cc_final: 0.6037 (mp0) REVERT: B 176 LYS cc_start: 0.6201 (tmmt) cc_final: 0.5867 (tmmt) REVERT: B 230 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6709 (mttp) REVERT: B 267 ARG cc_start: 0.7022 (mmt180) cc_final: 0.6777 (mmt-90) REVERT: B 291 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7117 (mp) REVERT: B 380 GLU cc_start: 0.6650 (tp30) cc_final: 0.6258 (mm-30) REVERT: B 397 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 525 LYS cc_start: 0.6844 (tptt) cc_final: 0.6519 (tptt) REVERT: B 561 GLN cc_start: 0.7346 (mt0) cc_final: 0.6572 (mp10) REVERT: B 569 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 633 CYS cc_start: 0.7378 (m) cc_final: 0.6799 (p) REVERT: B 690 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6761 (mm-30) REVERT: C 64 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6749 (pp20) REVERT: C 68 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7659 (tp) REVERT: C 194 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 229 GLU cc_start: 0.7062 (tt0) cc_final: 0.6821 (tt0) outliers start: 37 outliers final: 16 residues processed: 170 average time/residue: 1.3199 time to fit residues: 236.5877 Evaluate side-chains 173 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 281 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.0470 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7957 Z= 0.251 Angle : 0.535 7.710 10759 Z= 0.265 Chirality : 0.038 0.153 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.590 46.876 1050 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.97 % Allowed : 22.17 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.74 (0.27), residues: 957 helix: 1.61 (0.20), residues: 695 sheet: None (None), residues: 0 loop : 0.04 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 275 HIS 0.005 0.001 HIS B 48 PHE 0.019 0.002 PHE C 247 TYR 0.018 0.001 TYR B 355 ARG 0.005 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 216 GLN cc_start: 0.6945 (mt0) cc_final: 0.6721 (mt0) REVERT: B 127 GLU cc_start: 0.6357 (mp0) cc_final: 0.6070 (mp0) REVERT: B 230 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6678 (mttm) REVERT: B 256 LYS cc_start: 0.6666 (mmmt) cc_final: 0.6410 (mttt) REVERT: B 267 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6807 (mmt-90) REVERT: B 380 GLU cc_start: 0.6700 (tp30) cc_final: 0.6270 (mm-30) REVERT: B 397 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7180 (mt-10) REVERT: B 525 LYS cc_start: 0.6887 (tptt) cc_final: 0.6555 (tptt) REVERT: B 561 GLN cc_start: 0.7344 (mt0) cc_final: 0.6575 (mp10) REVERT: B 569 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7020 (mp) REVERT: B 586 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6013 (mtm180) REVERT: B 633 CYS cc_start: 0.7399 (m) cc_final: 0.7105 (p) REVERT: B 690 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7004 (mm-30) REVERT: C 64 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6750 (pp20) REVERT: C 68 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 152 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6590 (mmt) REVERT: C 194 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7514 (mm-30) REVERT: C 229 GLU cc_start: 0.7085 (tt0) cc_final: 0.6857 (tt0) outliers start: 34 outliers final: 18 residues processed: 177 average time/residue: 1.2460 time to fit residues: 232.9046 Evaluate side-chains 183 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 0.0170 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 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 97 ASN A 125 GLN B 108 ASN B 388 ASN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7957 Z= 0.245 Angle : 0.543 8.888 10759 Z= 0.267 Chirality : 0.038 0.153 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.565 47.344 1050 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.43 % Allowed : 21.94 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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 (0.27), residues: 957 helix: 1.65 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 296 HIS 0.004 0.001 HIS B 303 PHE 0.018 0.002 PHE C 247 TYR 0.017 0.001 TYR B 355 ARG 0.005 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 0.939 Fit side-chains REVERT: A 213 ASP cc_start: 0.6345 (m-30) cc_final: 0.5899 (m-30) REVERT: A 216 GLN cc_start: 0.6969 (mt0) cc_final: 0.6752 (mt0) REVERT: B 127 GLU cc_start: 0.6416 (mp0) cc_final: 0.6109 (mp0) REVERT: B 230 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6634 (mttp) REVERT: B 256 LYS cc_start: 0.6685 (mmmt) cc_final: 0.6479 (mttt) REVERT: B 267 ARG cc_start: 0.7045 (mmt180) cc_final: 0.6793 (mmt-90) REVERT: B 376 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5768 (mp0) REVERT: B 380 GLU cc_start: 0.6704 (tp30) cc_final: 0.6283 (mm-30) REVERT: B 397 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7154 (mt-10) REVERT: B 525 LYS cc_start: 0.6862 (tptt) cc_final: 0.6547 (tptt) REVERT: B 561 GLN cc_start: 0.7354 (mt0) cc_final: 0.6590 (mp10) REVERT: B 569 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7023 (mp) REVERT: B 690 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7018 (mm-30) REVERT: C 64 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6743 (pp20) REVERT: C 68 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7708 (tp) REVERT: C 229 GLU cc_start: 0.7071 (tt0) cc_final: 0.6852 (tt0) outliers start: 38 outliers final: 17 residues processed: 172 average time/residue: 1.2637 time to fit residues: 229.3840 Evaluate side-chains 168 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 197 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 65 ASN B 108 ASN B 148 GLN B 449 GLN B 554 ASN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7957 Z= 0.329 Angle : 0.591 10.023 10759 Z= 0.291 Chirality : 0.041 0.197 1231 Planarity : 0.004 0.044 1371 Dihedral : 4.703 46.917 1050 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.43 % Allowed : 22.52 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.54 (0.27), residues: 957 helix: 1.47 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.02 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 296 HIS 0.005 0.001 HIS B 303 PHE 0.020 0.002 PHE C 247 TYR 0.018 0.002 TYR B 355 ARG 0.006 0.001 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: A 213 ASP cc_start: 0.6368 (m-30) cc_final: 0.6061 (m-30) REVERT: A 216 GLN cc_start: 0.7003 (mt0) cc_final: 0.6774 (mt0) REVERT: B 127 GLU cc_start: 0.6531 (mp0) cc_final: 0.6115 (mp0) REVERT: B 230 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6482 (mtmm) REVERT: B 256 LYS cc_start: 0.6739 (mmmt) cc_final: 0.6508 (mttp) REVERT: B 267 ARG cc_start: 0.7037 (mmt180) cc_final: 0.6784 (mmt-90) REVERT: B 376 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: B 380 GLU cc_start: 0.6741 (tp30) cc_final: 0.6333 (mm-30) REVERT: B 397 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7167 (mt-10) REVERT: B 455 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7269 (p) REVERT: B 561 GLN cc_start: 0.7363 (mt0) cc_final: 0.6706 (mp10) REVERT: B 569 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7150 (mp) REVERT: B 633 CYS cc_start: 0.7440 (p) cc_final: 0.7103 (p) REVERT: B 642 ARG cc_start: 0.6723 (mtt90) cc_final: 0.6499 (mtt-85) REVERT: B 690 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 52 LEU cc_start: 0.6268 (mt) cc_final: 0.6037 (mp) REVERT: C 64 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6709 (pp20) REVERT: C 68 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7781 (tp) REVERT: C 229 GLU cc_start: 0.7065 (tt0) cc_final: 0.6850 (tt0) outliers start: 38 outliers final: 21 residues processed: 179 average time/residue: 1.2987 time to fit residues: 245.9530 Evaluate side-chains 177 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.0570 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 97 ASN B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7957 Z= 0.249 Angle : 0.552 8.623 10759 Z= 0.270 Chirality : 0.039 0.150 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.558 48.033 1050 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.73 % Allowed : 23.69 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.72 (0.27), residues: 957 helix: 1.62 (0.19), residues: 695 sheet: None (None), residues: 0 loop : -0.05 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 275 HIS 0.004 0.001 HIS B 303 PHE 0.017 0.002 PHE C 247 TYR 0.014 0.001 TYR B 355 ARG 0.006 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 0.889 Fit side-chains REVERT: A 29 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: A 213 ASP cc_start: 0.6250 (m-30) cc_final: 0.5881 (m-30) REVERT: A 216 GLN cc_start: 0.7028 (mt0) cc_final: 0.6788 (mt0) REVERT: A 223 LEU cc_start: 0.7797 (mt) cc_final: 0.7550 (mm) REVERT: B 127 GLU cc_start: 0.6581 (mp0) cc_final: 0.6186 (mp0) REVERT: B 230 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6458 (mtmm) REVERT: B 256 LYS cc_start: 0.6742 (mmmt) cc_final: 0.6490 (mttp) REVERT: B 267 ARG cc_start: 0.7055 (mmt180) cc_final: 0.6808 (mmt-90) REVERT: B 376 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: B 380 GLU cc_start: 0.6757 (tp30) cc_final: 0.6350 (mm-30) REVERT: B 397 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7186 (mt-10) REVERT: B 455 VAL cc_start: 0.7583 (OUTLIER) cc_final: 0.7283 (p) REVERT: B 561 GLN cc_start: 0.7363 (mt0) cc_final: 0.6700 (mp10) REVERT: B 569 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7019 (mp) REVERT: B 690 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7014 (mm-30) REVERT: C 52 LEU cc_start: 0.6264 (mt) cc_final: 0.6029 (mp) REVERT: C 64 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6727 (pp20) REVERT: C 68 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7752 (tp) REVERT: C 229 GLU cc_start: 0.7064 (tt0) cc_final: 0.6849 (tt0) outliers start: 32 outliers final: 18 residues processed: 177 average time/residue: 1.2058 time to fit residues: 225.7667 Evaluate side-chains 178 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0040 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 38 optimal weight: 0.0870 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 overall best weight: 0.1726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7957 Z= 0.173 Angle : 0.541 9.289 10759 Z= 0.264 Chirality : 0.037 0.185 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.439 49.530 1050 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 23.92 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.82 (0.27), residues: 957 helix: 1.76 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.27 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 263 HIS 0.004 0.001 HIS B 430 PHE 0.013 0.001 PHE C 247 TYR 0.012 0.001 TYR B 355 ARG 0.006 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: A 213 ASP cc_start: 0.6266 (m-30) cc_final: 0.5892 (m-30) REVERT: A 216 GLN cc_start: 0.7020 (mt0) cc_final: 0.6787 (mt0) REVERT: B 127 GLU cc_start: 0.6581 (mp0) cc_final: 0.6163 (mp0) REVERT: B 230 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6427 (mtmm) REVERT: B 256 LYS cc_start: 0.6722 (mmmt) cc_final: 0.6488 (mttp) REVERT: B 267 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6799 (mmt-90) REVERT: B 376 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: B 380 GLU cc_start: 0.6777 (tp30) cc_final: 0.6370 (mm-30) REVERT: B 397 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 455 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 459 GLU cc_start: 0.7154 (mp0) cc_final: 0.6786 (mp0) REVERT: B 561 GLN cc_start: 0.7326 (mt0) cc_final: 0.6665 (mp10) REVERT: B 569 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7007 (mp) REVERT: B 690 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6994 (mm-30) REVERT: C 52 LEU cc_start: 0.6237 (mt) cc_final: 0.6015 (mp) REVERT: C 64 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6743 (pp20) REVERT: C 68 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7699 (tp) REVERT: C 229 GLU cc_start: 0.7056 (tt0) cc_final: 0.6841 (tt0) outliers start: 29 outliers final: 14 residues processed: 170 average time/residue: 1.2209 time to fit residues: 219.4040 Evaluate side-chains 171 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0570 chunk 56 optimal weight: 0.0370 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 48 HIS ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 554 ASN B 632 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7957 Z= 0.198 Angle : 0.547 11.493 10759 Z= 0.264 Chirality : 0.038 0.160 1231 Planarity : 0.004 0.044 1371 Dihedral : 4.402 49.964 1050 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.80 % Allowed : 24.39 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.86 (0.27), residues: 957 helix: 1.79 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 263 HIS 0.004 0.001 HIS B 430 PHE 0.015 0.001 PHE C 247 TYR 0.011 0.001 TYR B 355 ARG 0.006 0.000 ARG B 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: A 213 ASP cc_start: 0.6256 (m-30) cc_final: 0.5882 (m-30) REVERT: A 216 GLN cc_start: 0.7031 (mt0) cc_final: 0.6794 (mt0) REVERT: A 236 MET cc_start: 0.7148 (mtp) cc_final: 0.6895 (mtm) REVERT: B 127 GLU cc_start: 0.6566 (mp0) cc_final: 0.6156 (mp0) REVERT: B 230 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6456 (mtmm) REVERT: B 256 LYS cc_start: 0.6748 (mmmt) cc_final: 0.6502 (mttp) REVERT: B 267 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6805 (mmt-90) REVERT: B 376 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5711 (mp0) REVERT: B 380 GLU cc_start: 0.6772 (tp30) cc_final: 0.6343 (mm-30) REVERT: B 397 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 455 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7276 (p) REVERT: B 561 GLN cc_start: 0.7344 (mt0) cc_final: 0.6705 (mp10) REVERT: B 569 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 690 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7008 (mm-30) REVERT: C 52 LEU cc_start: 0.6217 (mt) cc_final: 0.5995 (mp) REVERT: C 64 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6745 (pp20) REVERT: C 68 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7735 (tp) REVERT: C 229 GLU cc_start: 0.7061 (tt0) cc_final: 0.6844 (tt0) outliers start: 24 outliers final: 15 residues processed: 171 average time/residue: 1.1937 time to fit residues: 215.8869 Evaluate side-chains 178 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 665 CYS Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0040 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 48 HIS B 108 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130212 restraints weight = 9834.841| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.56 r_work: 0.3617 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7957 Z= 0.229 Angle : 0.561 10.994 10759 Z= 0.272 Chirality : 0.039 0.160 1231 Planarity : 0.004 0.043 1371 Dihedral : 4.444 50.363 1050 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 24.62 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1.78 (0.27), residues: 957 helix: 1.74 (0.19), residues: 705 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.004 0.001 HIS B 430 PHE 0.016 0.002 PHE C 247 TYR 0.013 0.001 TYR B 136 ARG 0.006 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.67 seconds wall clock time: 72 minutes 52.72 seconds (4372.72 seconds total)