Starting phenix.real_space_refine on Thu Mar 13 04:25:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcm_38247/03_2025/8xcm_38247.cif" } resolution = 3.08 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5422 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4168 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 53.333 64.114 34.976 1.00127.49 S ATOM 1738 SG CYS A 222 53.792 68.828 30.722 1.00131.05 S ATOM 1698 SG CYS A 216 52.555 63.628 28.263 1.00131.75 S Time building chain proxies: 5.49, per 1000 atoms: 0.64 Number of scatterers: 8605 At special positions: 0 Unit cell: (104.06, 108.36, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5422 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 - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 40.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.584A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.556A pdb=" N TYR A 96 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.171A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.883A pdb=" N ARG A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 441 through 463 removed outlier: 3.739A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 104 through 111 removed outlier: 3.791A pdb=" N LEU B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.848A pdb=" N VAL B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.547A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 57' Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.746A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 447 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.464A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.618A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.297A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 259 removed outlier: 6.280A pdb=" N VAL A 254 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 270 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA A 256 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 268 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 258 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 270 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 387 through 388 304 hydrogen bonds defined for protein. 849 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: 2.10 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8746 1.76 - 2.30: 90 2.30 - 2.84: 0 2.84 - 3.38: 0 3.38 - 3.92: 3 Bond restraints: 8839 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.922 -1.622 2.00e-02 2.50e+03 6.58e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.801 -1.543 2.00e-02 2.50e+03 5.95e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.708 -1.475 2.00e-02 2.50e+03 5.44e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.38: 12065 9.38 - 18.75: 8 18.75 - 28.13: 0 28.13 - 37.51: 8 37.51 - 46.89: 2 Bond angle restraints: 12083 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.86 46.89 3.00e+00 1.11e-01 2.44e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 71.35 41.24 3.00e+00 1.11e-01 1.89e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 67.65 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 38.28 33.47 3.00e+00 1.11e-01 1.24e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 38.78 33.31 3.00e+00 1.11e-01 1.23e+02 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4442 17.92 - 35.84: 588 35.84 - 53.76: 160 53.76 - 71.68: 24 71.68 - 89.60: 13 Dihedral angle restraints: 5227 sinusoidal: 2075 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ALA C 117 " pdb=" C ALA C 117 " pdb=" N MET C 118 " pdb=" CA MET C 118 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 395 " pdb=" C MET C 395 " pdb=" N PRO C 396 " pdb=" CA PRO C 396 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" C2C HEC C 503 " pdb=" C3C HEC C 503 " pdb=" CAC HEC C 503 " pdb=" CBC HEC C 503 " ideal model delta sinusoidal sigma weight residual 60.00 11.00 49.00 2 1.00e+01 1.00e-02 2.73e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.271: 1276 3.271 - 6.543: 0 6.543 - 9.814: 0 9.814 - 13.085: 0 13.085 - 16.356: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -5.59 16.36 2.00e-01 2.50e+01 6.69e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 118 " -0.083 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO B 119 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.022 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" CGD HEC C 501 " 0.082 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.030 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 311 " 0.070 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO C 312 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 312 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 312 " 0.055 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 252 2.67 - 3.23: 8905 3.23 - 3.79: 14843 3.79 - 4.34: 19937 4.34 - 4.90: 31824 Nonbonded interactions: 75761 Sorted by model distance: nonbonded pdb=" OH TYR A 79 " pdb=" O GLN A 98 " model vdw 2.118 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" OG SER A 522 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 145 " pdb=" OD2 ASP A 535 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN A 369 " pdb=" OG1 THR A 371 " model vdw 2.187 3.040 ... (remaining 75756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.740 Find NCS groups from input model: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.030 1.622 8839 Z= 1.402 Angle : 1.333 46.886 12083 Z= 0.534 Chirality : 0.460 16.356 1277 Planarity : 0.007 0.120 1569 Dihedral : 17.720 89.597 3215 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.68 % Allowed : 29.23 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1083 helix: 1.25 (0.28), residues: 375 sheet: -1.91 (0.65), residues: 58 loop : -0.59 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 51 HIS 0.006 0.001 HIS A 110 PHE 0.012 0.001 PHE A 270 TYR 0.023 0.002 TYR A 271 ARG 0.008 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8366 (t0) cc_final: 0.7955 (m-30) REVERT: A 146 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 262 LYS cc_start: 0.9159 (tptp) cc_final: 0.8807 (tppt) REVERT: A 490 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7776 (pmt-80) REVERT: B 141 VAL cc_start: 0.8530 (t) cc_final: 0.8256 (p) REVERT: B 169 TYR cc_start: 0.9015 (p90) cc_final: 0.8719 (p90) REVERT: C 120 TYR cc_start: 0.8736 (p90) cc_final: 0.8387 (p90) REVERT: C 172 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7719 (mmt-90) outliers start: 6 outliers final: 2 residues processed: 144 average time/residue: 0.2152 time to fit residues: 42.8459 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 332 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 168 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.067924 restraints weight = 18081.137| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.20 r_work: 0.2784 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 8839 Z= 0.393 Angle : 1.149 86.326 12083 Z= 0.456 Chirality : 0.068 1.731 1277 Planarity : 0.006 0.066 1569 Dihedral : 9.262 79.591 1288 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.72 % Allowed : 23.93 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1083 helix: 1.27 (0.28), residues: 381 sheet: -1.30 (0.59), residues: 70 loop : -0.63 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 PHE 0.023 0.002 PHE A 80 TYR 0.016 0.002 TYR A 271 ARG 0.006 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8917 (mtp) cc_final: 0.8546 (mtp) REVERT: A 221 ASN cc_start: 0.8541 (t0) cc_final: 0.7978 (t0) REVERT: A 262 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8901 (tppp) REVERT: A 266 THR cc_start: 0.8597 (m) cc_final: 0.8340 (p) REVERT: A 305 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7286 (ttm110) REVERT: A 456 MET cc_start: 0.8758 (mmm) cc_final: 0.8552 (tpp) REVERT: A 478 HIS cc_start: 0.7817 (m170) cc_final: 0.7617 (m170) REVERT: A 535 ASP cc_start: 0.8594 (t0) cc_final: 0.8014 (m-30) REVERT: B 49 ASP cc_start: 0.8471 (m-30) cc_final: 0.8075 (t0) REVERT: B 100 ASN cc_start: 0.8389 (t0) cc_final: 0.8101 (t0) REVERT: B 141 VAL cc_start: 0.8816 (t) cc_final: 0.8607 (p) REVERT: B 173 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8510 (mm-30) REVERT: B 180 MET cc_start: 0.8957 (mmm) cc_final: 0.8612 (mmm) REVERT: C 118 MET cc_start: 0.8824 (tpt) cc_final: 0.8266 (tpt) REVERT: C 395 MET cc_start: 0.8576 (tpt) cc_final: 0.8238 (tpt) REVERT: C 410 GLU cc_start: 0.8757 (tp30) cc_final: 0.8544 (tp30) outliers start: 33 outliers final: 21 residues processed: 157 average time/residue: 0.2025 time to fit residues: 44.4948 Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.073066 restraints weight = 17889.104| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.24 r_work: 0.2874 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 8839 Z= 0.220 Angle : 1.052 83.066 12083 Z= 0.409 Chirality : 0.061 1.504 1277 Planarity : 0.005 0.057 1569 Dihedral : 8.654 82.073 1287 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.29 % Allowed : 22.46 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1083 helix: 1.48 (0.28), residues: 380 sheet: -1.37 (0.60), residues: 74 loop : -0.55 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.012 0.001 PHE B 60 TYR 0.016 0.001 TYR A 271 ARG 0.004 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8690 (tp40) cc_final: 0.8298 (tp-100) REVERT: A 57 ASP cc_start: 0.8439 (t0) cc_final: 0.7913 (m-30) REVERT: A 156 MET cc_start: 0.8642 (mtp) cc_final: 0.8224 (mtp) REVERT: A 175 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.6960 (mmt) REVERT: A 221 ASN cc_start: 0.8441 (t0) cc_final: 0.7754 (t0) REVERT: A 266 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 305 ARG cc_start: 0.8485 (tpt90) cc_final: 0.7392 (ttm110) REVERT: A 535 ASP cc_start: 0.8569 (t0) cc_final: 0.8067 (m-30) REVERT: B 49 ASP cc_start: 0.8416 (m-30) cc_final: 0.8065 (t0) REVERT: B 100 ASN cc_start: 0.8407 (t0) cc_final: 0.8186 (t0) REVERT: B 141 VAL cc_start: 0.8600 (t) cc_final: 0.8363 (p) REVERT: B 173 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8494 (mm-30) REVERT: C 118 MET cc_start: 0.8690 (tpt) cc_final: 0.7727 (tpt) REVERT: C 211 LEU cc_start: 0.9389 (tp) cc_final: 0.9126 (tt) REVERT: C 395 MET cc_start: 0.8127 (tpt) cc_final: 0.7817 (tpt) REVERT: C 410 GLU cc_start: 0.8830 (tp30) cc_final: 0.8622 (tp30) outliers start: 38 outliers final: 21 residues processed: 166 average time/residue: 0.1940 time to fit residues: 45.9227 Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.070991 restraints weight = 17911.607| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.15 r_work: 0.2838 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8839 Z= 0.306 Angle : 1.077 83.949 12083 Z= 0.420 Chirality : 0.061 1.476 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.760 83.213 1287 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.30 % Allowed : 22.23 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1083 helix: 1.60 (0.28), residues: 380 sheet: -1.20 (0.62), residues: 72 loop : -0.56 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 PHE 0.018 0.001 PHE A 80 TYR 0.015 0.001 TYR A 271 ARG 0.007 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.9067 (t0) cc_final: 0.8825 (t0) REVERT: A 156 MET cc_start: 0.8792 (mtp) cc_final: 0.8384 (mtp) REVERT: A 175 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.6922 (mmt) REVERT: A 247 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7729 (tttm) REVERT: A 305 ARG cc_start: 0.8537 (tpt90) cc_final: 0.7442 (ttm110) REVERT: A 419 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 477 GLN cc_start: 0.8775 (mp10) cc_final: 0.8489 (mp10) REVERT: A 535 ASP cc_start: 0.8565 (t0) cc_final: 0.8084 (m-30) REVERT: B 49 ASP cc_start: 0.8376 (m-30) cc_final: 0.8043 (t0) REVERT: B 100 ASN cc_start: 0.8420 (t0) cc_final: 0.8166 (t0) REVERT: B 136 GLU cc_start: 0.8989 (pm20) cc_final: 0.8599 (pm20) REVERT: B 141 VAL cc_start: 0.8717 (t) cc_final: 0.8488 (p) REVERT: B 173 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 177 VAL cc_start: 0.8802 (m) cc_final: 0.8491 (t) REVERT: C 118 MET cc_start: 0.8734 (tpt) cc_final: 0.7909 (tpt) REVERT: C 211 LEU cc_start: 0.9398 (tp) cc_final: 0.9005 (tt) REVERT: C 395 MET cc_start: 0.8292 (tpt) cc_final: 0.7614 (tpt) outliers start: 47 outliers final: 30 residues processed: 157 average time/residue: 0.1862 time to fit residues: 42.1349 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.069586 restraints weight = 17790.957| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.01 r_work: 0.2816 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 8839 Z= 0.311 Angle : 1.074 83.872 12083 Z= 0.418 Chirality : 0.061 1.487 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.751 84.820 1287 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.19 % Allowed : 22.23 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1083 helix: 1.65 (0.28), residues: 380 sheet: -1.16 (0.64), residues: 72 loop : -0.56 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 PHE 0.017 0.001 PHE A 80 TYR 0.015 0.002 TYR A 271 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: A 84 ASN cc_start: 0.9090 (t0) cc_final: 0.8858 (t0) REVERT: A 156 MET cc_start: 0.8652 (mtp) cc_final: 0.8237 (mtp) REVERT: A 175 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.6836 (mmt) REVERT: A 221 ASN cc_start: 0.8540 (t0) cc_final: 0.7697 (t0) REVERT: A 247 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7777 (tttm) REVERT: A 305 ARG cc_start: 0.8650 (tpt90) cc_final: 0.7581 (ttm110) REVERT: A 535 ASP cc_start: 0.8602 (t0) cc_final: 0.8161 (m-30) REVERT: B 49 ASP cc_start: 0.8423 (m-30) cc_final: 0.8086 (t0) REVERT: B 83 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.6040 (ptmm) REVERT: B 100 ASN cc_start: 0.8456 (t0) cc_final: 0.8238 (t0) REVERT: B 141 VAL cc_start: 0.8711 (t) cc_final: 0.8484 (p) REVERT: B 173 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8570 (mm-30) REVERT: C 118 MET cc_start: 0.8759 (tpt) cc_final: 0.7850 (tpt) REVERT: C 161 ARG cc_start: 0.8508 (ptp-110) cc_final: 0.7754 (ttm110) REVERT: C 211 LEU cc_start: 0.9383 (tp) cc_final: 0.8982 (tt) REVERT: C 395 MET cc_start: 0.8333 (tpt) cc_final: 0.7846 (tpt) outliers start: 46 outliers final: 34 residues processed: 154 average time/residue: 0.1942 time to fit residues: 42.3949 Evaluate side-chains 147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.071892 restraints weight = 17529.906| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.94 r_work: 0.2866 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8839 Z= 0.244 Angle : 1.052 83.707 12083 Z= 0.406 Chirality : 0.060 1.478 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.645 86.005 1287 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.40 % Allowed : 23.81 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1083 helix: 1.68 (0.28), residues: 380 sheet: -1.17 (0.64), residues: 72 loop : -0.54 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 503 PHE 0.016 0.001 PHE B 60 TYR 0.014 0.001 TYR A 271 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 84 ASN cc_start: 0.9026 (t0) cc_final: 0.8718 (t0) REVERT: A 156 MET cc_start: 0.8649 (mtp) cc_final: 0.8256 (mtp) REVERT: A 175 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.6977 (mmt) REVERT: A 221 ASN cc_start: 0.8566 (t0) cc_final: 0.7643 (t0) REVERT: A 247 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7740 (tttm) REVERT: A 305 ARG cc_start: 0.8672 (tpt90) cc_final: 0.7489 (ttm110) REVERT: A 320 ASN cc_start: 0.7509 (t0) cc_final: 0.6946 (t0) REVERT: A 535 ASP cc_start: 0.8536 (t0) cc_final: 0.8104 (m-30) REVERT: B 49 ASP cc_start: 0.8389 (m-30) cc_final: 0.8050 (t70) REVERT: B 83 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5973 (ptmm) REVERT: B 104 ASP cc_start: 0.8415 (m-30) cc_final: 0.7504 (p0) REVERT: B 136 GLU cc_start: 0.9071 (pm20) cc_final: 0.8787 (pm20) REVERT: B 141 VAL cc_start: 0.8660 (t) cc_final: 0.8430 (p) REVERT: B 173 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 177 VAL cc_start: 0.8851 (m) cc_final: 0.8581 (t) REVERT: C 118 MET cc_start: 0.8749 (tpt) cc_final: 0.7872 (tpt) REVERT: C 161 ARG cc_start: 0.8573 (ptp-110) cc_final: 0.7927 (ttm110) REVERT: C 328 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8420 (p) REVERT: C 395 MET cc_start: 0.8262 (tpt) cc_final: 0.7685 (tpt) outliers start: 39 outliers final: 33 residues processed: 154 average time/residue: 0.1982 time to fit residues: 43.1386 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.071866 restraints weight = 17816.827| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.04 r_work: 0.2861 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8839 Z= 0.247 Angle : 1.051 83.753 12083 Z= 0.406 Chirality : 0.060 1.474 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.599 86.694 1287 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.53 % Allowed : 23.48 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1083 helix: 1.78 (0.28), residues: 376 sheet: -1.23 (0.64), residues: 73 loop : -0.48 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.018 0.001 PHE C 210 TYR 0.014 0.001 TYR A 271 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: A 84 ASN cc_start: 0.9005 (t0) cc_final: 0.8668 (t0) REVERT: A 156 MET cc_start: 0.8627 (mtp) cc_final: 0.8227 (mtp) REVERT: A 175 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.6985 (mmt) REVERT: A 221 ASN cc_start: 0.8566 (t0) cc_final: 0.7625 (t0) REVERT: A 247 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7772 (tttm) REVERT: A 305 ARG cc_start: 0.8675 (tpt90) cc_final: 0.7526 (ttm110) REVERT: A 320 ASN cc_start: 0.7403 (t0) cc_final: 0.6842 (t0) REVERT: A 535 ASP cc_start: 0.8547 (t0) cc_final: 0.8125 (m-30) REVERT: B 49 ASP cc_start: 0.8384 (m-30) cc_final: 0.8069 (t70) REVERT: B 83 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6002 (ptmm) REVERT: B 104 ASP cc_start: 0.8451 (m-30) cc_final: 0.7470 (p0) REVERT: B 136 GLU cc_start: 0.9096 (pm20) cc_final: 0.8805 (pm20) REVERT: B 141 VAL cc_start: 0.8652 (t) cc_final: 0.8429 (p) REVERT: B 173 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8686 (mm-30) REVERT: B 177 VAL cc_start: 0.8869 (m) cc_final: 0.8617 (t) REVERT: C 118 MET cc_start: 0.8741 (tpt) cc_final: 0.7858 (tpt) REVERT: C 161 ARG cc_start: 0.8535 (ptp-110) cc_final: 0.7641 (ttm110) REVERT: C 328 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8408 (p) outliers start: 49 outliers final: 38 residues processed: 159 average time/residue: 0.2040 time to fit residues: 46.4770 Evaluate side-chains 156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 411 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072951 restraints weight = 18040.957| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.98 r_work: 0.2880 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8839 Z= 0.235 Angle : 1.048 83.743 12083 Z= 0.404 Chirality : 0.060 1.472 1277 Planarity : 0.005 0.063 1569 Dihedral : 8.545 87.354 1287 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.97 % Allowed : 23.48 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1083 helix: 1.84 (0.28), residues: 370 sheet: -1.32 (0.59), residues: 83 loop : -0.43 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.019 0.001 PHE B 60 TYR 0.026 0.001 TYR A 79 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: A 84 ASN cc_start: 0.8960 (t0) cc_final: 0.8557 (t0) REVERT: A 156 MET cc_start: 0.8642 (mtp) cc_final: 0.8287 (mtp) REVERT: A 175 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7065 (mmt) REVERT: A 221 ASN cc_start: 0.8587 (t0) cc_final: 0.7501 (t0) REVERT: A 247 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7777 (tttm) REVERT: A 305 ARG cc_start: 0.8696 (tpt90) cc_final: 0.7565 (ttm110) REVERT: A 526 MET cc_start: 0.8237 (mtm) cc_final: 0.7876 (mtt) REVERT: A 535 ASP cc_start: 0.8521 (t0) cc_final: 0.8129 (m-30) REVERT: B 49 ASP cc_start: 0.8351 (m-30) cc_final: 0.8045 (t70) REVERT: B 83 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5890 (ptmm) REVERT: B 104 ASP cc_start: 0.8488 (m-30) cc_final: 0.7595 (p0) REVERT: B 123 GLN cc_start: 0.8520 (tt0) cc_final: 0.8268 (tt0) REVERT: B 136 GLU cc_start: 0.9093 (pm20) cc_final: 0.8809 (pm20) REVERT: B 141 VAL cc_start: 0.8658 (t) cc_final: 0.8429 (p) REVERT: B 173 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8693 (mm-30) REVERT: B 177 VAL cc_start: 0.8919 (m) cc_final: 0.8689 (t) REVERT: C 118 MET cc_start: 0.8749 (tpt) cc_final: 0.7922 (tpt) REVERT: C 161 ARG cc_start: 0.8542 (ptp-110) cc_final: 0.7772 (ttm110) REVERT: C 182 HIS cc_start: 0.9179 (m90) cc_final: 0.8951 (m-70) REVERT: C 315 TYR cc_start: 0.7854 (p90) cc_final: 0.7650 (p90) REVERT: C 328 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8383 (p) outliers start: 44 outliers final: 38 residues processed: 157 average time/residue: 0.1994 time to fit residues: 44.2997 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 411 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073552 restraints weight = 17955.350| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.98 r_work: 0.2896 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8839 Z= 0.231 Angle : 1.052 83.730 12083 Z= 0.405 Chirality : 0.060 1.467 1277 Planarity : 0.005 0.056 1569 Dihedral : 8.412 87.826 1285 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.85 % Allowed : 23.81 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1083 helix: 1.84 (0.28), residues: 370 sheet: -0.90 (0.66), residues: 69 loop : -0.45 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.020 0.001 PHE B 60 TYR 0.023 0.001 TYR A 79 ARG 0.004 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8924 (t0) cc_final: 0.8513 (t0) REVERT: A 156 MET cc_start: 0.8663 (mtp) cc_final: 0.8344 (mtp) REVERT: A 175 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7130 (mmt) REVERT: A 221 ASN cc_start: 0.8594 (t0) cc_final: 0.7530 (t0) REVERT: A 247 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7764 (tttm) REVERT: A 305 ARG cc_start: 0.8681 (tpt90) cc_final: 0.7516 (ttm110) REVERT: A 320 ASN cc_start: 0.6816 (t0) cc_final: 0.6532 (t0) REVERT: A 526 MET cc_start: 0.8244 (mtm) cc_final: 0.7916 (mtt) REVERT: A 535 ASP cc_start: 0.8523 (t0) cc_final: 0.8138 (m-30) REVERT: B 49 ASP cc_start: 0.8348 (m-30) cc_final: 0.8048 (t70) REVERT: B 83 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5918 (ptmm) REVERT: B 104 ASP cc_start: 0.8515 (m-30) cc_final: 0.7679 (p0) REVERT: B 123 GLN cc_start: 0.8549 (tt0) cc_final: 0.8331 (tt0) REVERT: B 136 GLU cc_start: 0.9087 (pm20) cc_final: 0.8805 (pm20) REVERT: B 141 VAL cc_start: 0.8659 (t) cc_final: 0.8418 (p) REVERT: B 173 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 177 VAL cc_start: 0.8932 (m) cc_final: 0.8722 (t) REVERT: C 118 MET cc_start: 0.8685 (tpt) cc_final: 0.8095 (tpt) REVERT: C 160 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8871 (pt) REVERT: C 161 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.8033 (ttm170) REVERT: C 182 HIS cc_start: 0.9168 (m90) cc_final: 0.8934 (m-70) REVERT: C 328 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8373 (p) REVERT: C 394 LEU cc_start: 0.8253 (tp) cc_final: 0.7976 (tp) REVERT: C 395 MET cc_start: 0.8103 (tpt) cc_final: 0.7801 (tpt) outliers start: 43 outliers final: 37 residues processed: 161 average time/residue: 0.2027 time to fit residues: 46.1354 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 411 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.072378 restraints weight = 18004.546| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.00 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8839 Z= 0.257 Angle : 1.062 83.873 12083 Z= 0.411 Chirality : 0.060 1.469 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.456 88.443 1285 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.74 % Allowed : 23.70 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 1083 helix: 1.83 (0.28), residues: 370 sheet: -0.92 (0.66), residues: 69 loop : -0.45 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.022 0.002 PHE B 60 TYR 0.023 0.001 TYR A 79 ARG 0.004 0.000 ARG A 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8885 (t0) cc_final: 0.8478 (t0) REVERT: A 156 MET cc_start: 0.8708 (mtp) cc_final: 0.8328 (mtp) REVERT: A 175 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: A 221 ASN cc_start: 0.8567 (t0) cc_final: 0.7612 (t0) REVERT: A 247 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7778 (tttm) REVERT: A 305 ARG cc_start: 0.8690 (tpt90) cc_final: 0.7507 (ttm110) REVERT: A 320 ASN cc_start: 0.6780 (t0) cc_final: 0.6489 (t0) REVERT: A 526 MET cc_start: 0.8241 (mtm) cc_final: 0.7610 (mtt) REVERT: A 535 ASP cc_start: 0.8541 (t0) cc_final: 0.8158 (m-30) REVERT: B 49 ASP cc_start: 0.8320 (m-30) cc_final: 0.7993 (t70) REVERT: B 83 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5901 (ptmm) REVERT: B 104 ASP cc_start: 0.8501 (m-30) cc_final: 0.7594 (p0) REVERT: B 123 GLN cc_start: 0.8548 (tt0) cc_final: 0.8324 (tt0) REVERT: B 136 GLU cc_start: 0.9108 (pm20) cc_final: 0.8829 (pm20) REVERT: B 141 VAL cc_start: 0.8722 (t) cc_final: 0.8494 (p) REVERT: B 173 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8706 (mm-30) REVERT: B 177 VAL cc_start: 0.8926 (m) cc_final: 0.8722 (t) REVERT: C 118 MET cc_start: 0.8770 (tpt) cc_final: 0.8181 (tpt) REVERT: C 161 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7843 (ttm110) REVERT: C 182 HIS cc_start: 0.9178 (m90) cc_final: 0.8945 (m-70) REVERT: C 328 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8378 (p) REVERT: C 395 MET cc_start: 0.8151 (tpt) cc_final: 0.7748 (tpt) outliers start: 42 outliers final: 37 residues processed: 158 average time/residue: 0.1877 time to fit residues: 41.9849 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 411 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072591 restraints weight = 18016.443| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.99 r_work: 0.2876 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8839 Z= 0.246 Angle : 1.058 83.764 12083 Z= 0.410 Chirality : 0.060 1.470 1277 Planarity : 0.005 0.054 1569 Dihedral : 8.452 88.910 1285 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.63 % Allowed : 24.15 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1083 helix: 1.81 (0.28), residues: 371 sheet: -1.22 (0.60), residues: 83 loop : -0.43 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.016 0.001 PHE C 210 TYR 0.022 0.001 TYR A 79 ARG 0.004 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.09 seconds wall clock time: 69 minutes 35.78 seconds (4175.78 seconds total)