Starting phenix.real_space_refine on Mon May 12 01:40:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcm_38247/05_2025/8xcm_38247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcm_38247/05_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_38247/05_2025/8xcm_38247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcm_38247/05_2025/8xcm_38247.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcm_38247/05_2025/8xcm_38247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcm_38247/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.97, per 1000 atoms: 0.69 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: 2.93 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: 0.86 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: 2.22 Time building geometry restraints manager: 3.26 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.660 Find NCS groups from input model: 0.080 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: 30.060 ------------------------------------------------------------------------------- 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 8854 Z= 1.468 Angle : 1.375 46.886 12092 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 Details of bonding type rmsd hydrogen bonds : bond 0.16807 ( 304) hydrogen bonds : angle 6.94723 ( 849) metal coordination : bond 0.00238 ( 3) metal coordination : angle 12.47362 ( 9) covalent geometry : bond 0.02960 ( 8839) covalent geometry : angle 1.33282 (12083) Misc. bond : bond 0.06990 ( 12) *********************** 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 : 0.938 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: 0.2091 time to fit residues: 41.3124 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 : 0.927 ------------------------------------------------------------------------------- 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 = 0.067922 restraints weight = 18081.136| |-----------------------------------------------------------------------------| 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 : 0.007 0.211 8854 Z= 0.248 Angle : 1.540 86.326 12092 Z= 0.463 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 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 304) hydrogen bonds : angle 5.39717 ( 849) metal coordination : bond 0.01358 ( 3) metal coordination : angle 37.63449 ( 9) covalent geometry : bond 0.00597 ( 8839) covalent geometry : angle 1.14862 (12083) Misc. bond : bond 0.08806 ( 12) *********************** 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 : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8917 (mtp) cc_final: 0.8547 (mtp) REVERT: A 221 ASN cc_start: 0.8540 (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: 0.8341 (p) REVERT: A 305 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7286 (ttm110) REVERT: A 456 MET cc_start: 0.8759 (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: 0.8593 (t0) cc_final: 0.8013 (m-30) REVERT: B 49 ASP cc_start: 0.8470 (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: 0.8606 (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: 0.8267 (tpt) REVERT: C 395 MET cc_start: 0.8576 (tpt) cc_final: 0.8239 (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: 0.2163 time to fit residues: 47.4253 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 : 0.969 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.071457 restraints weight = 17972.894| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.20 r_work: 0.2845 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 8854 Z= 0.160 Angle : 1.424 83.330 12092 Z= 0.419 Chirality : 0.061 1.497 1277 Planarity : 0.005 0.057 1569 Dihedral : 8.722 82.172 1287 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.74 % Allowed : 22.12 % Favored : 73.14 % 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: 0.15 (0.26), residues: 1083 helix: 1.48 (0.28), residues: 380 sheet: -1.40 (0.59), residues: 74 loop : -0.56 (0.25), residues: 629 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 0.012 0.001 PHE B 60 TYR 0.016 0.001 TYR A 271 ARG 0.005 0.000 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 304) hydrogen bonds : angle 5.05615 ( 849) metal coordination : bond 0.00213 ( 3) metal coordination : angle 34.91355 ( 9) covalent geometry : bond 0.00384 ( 8839) covalent geometry : angle 1.05950 (12083) Misc. bond : bond 0.05031 ( 12) *********************** 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 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8713 (tp40) cc_final: 0.8349 (tp-100) REVERT: A 57 ASP cc_start: 0.8479 (t0) cc_final: 0.7947 (m-30) REVERT: A 156 MET cc_start: 0.8670 (mtp) cc_final: 0.8236 (mtp) REVERT: A 175 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.6950 (mmt) REVERT: A 221 ASN cc_start: 0.8530 (t0) cc_final: 0.7813 (t0) REVERT: A 266 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 305 ARG cc_start: 0.8486 (tpt90) cc_final: 0.7421 (ttm110) REVERT: A 535 ASP cc_start: 0.8566 (t0) cc_final: 0.8033 (m-30) REVERT: B 49 ASP cc_start: 0.8421 (m-30) cc_final: 0.8072 (t0) REVERT: B 100 ASN cc_start: 0.8417 (t0) cc_final: 0.8200 (t0) REVERT: B 141 VAL cc_start: 0.8649 (t) cc_final: 0.8426 (p) REVERT: B 173 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 180 MET cc_start: 0.8896 (mmm) cc_final: 0.8691 (mmm) REVERT: C 118 MET cc_start: 0.8708 (tpt) cc_final: 0.7739 (tpt) REVERT: C 211 LEU cc_start: 0.9392 (tp) cc_final: 0.9125 (tt) REVERT: C 395 MET cc_start: 0.8273 (tpt) cc_final: 0.7735 (tpt) outliers start: 42 outliers final: 24 residues processed: 162 average time/residue: 0.1971 time to fit residues: 44.9745 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 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 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 364 THR 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 A residue 505 ASN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN 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 = 0.3300 r_free = 0.3300 target = 0.090268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.072391 restraints weight = 17825.635| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.16 r_work: 0.2864 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 8854 Z= 0.169 Angle : 1.428 83.660 12092 Z= 0.419 Chirality : 0.061 1.483 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.683 83.016 1287 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.08 % Allowed : 21.78 % Favored : 73.14 % 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: -1.24 (0.61), 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 110 PHE 0.014 0.001 PHE A 80 TYR 0.015 0.001 TYR A 271 ARG 0.005 0.000 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 304) hydrogen bonds : angle 4.95174 ( 849) metal coordination : bond 0.00315 ( 3) metal coordination : angle 35.01991 ( 9) covalent geometry : bond 0.00407 ( 8839) covalent geometry : angle 1.06124 (12083) Misc. bond : bond 0.04546 ( 12) *********************** 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 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.9099 (t0) cc_final: 0.8843 (t0) REVERT: A 156 MET cc_start: 0.8751 (mtp) cc_final: 0.8361 (mtp) REVERT: A 175 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.6981 (mmt) REVERT: A 221 ASN cc_start: 0.8495 (t0) cc_final: 0.7710 (t0) REVERT: A 247 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7668 (tttm) REVERT: A 266 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 305 ARG cc_start: 0.8523 (tpt90) cc_final: 0.7435 (ttm110) REVERT: A 477 GLN cc_start: 0.8763 (mp10) cc_final: 0.8479 (mp10) REVERT: A 505 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8330 (p0) REVERT: A 535 ASP cc_start: 0.8587 (t0) cc_final: 0.8084 (m-30) REVERT: B 49 ASP cc_start: 0.8384 (m-30) cc_final: 0.8056 (t0) REVERT: B 100 ASN cc_start: 0.8418 (t0) cc_final: 0.8170 (t0) REVERT: B 136 GLU cc_start: 0.9000 (pm20) cc_final: 0.8634 (pm20) REVERT: B 141 VAL cc_start: 0.8682 (t) cc_final: 0.8456 (p) REVERT: B 173 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8561 (mm-30) REVERT: C 118 MET cc_start: 0.8743 (tpt) cc_final: 0.7885 (tpt) REVERT: C 211 LEU cc_start: 0.9400 (tp) cc_final: 0.9010 (tt) REVERT: C 395 MET cc_start: 0.8227 (tpt) cc_final: 0.7664 (tpt) outliers start: 45 outliers final: 28 residues processed: 155 average time/residue: 0.1936 time to fit residues: 42.5382 Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 266 THR 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 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 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: 3.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** A 505 ASN 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 = 0.3243 r_free = 0.3243 target = 0.086667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.069058 restraints weight = 17749.035| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.98 r_work: 0.2812 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 8854 Z= 0.213 Angle : 1.459 83.925 12092 Z= 0.429 Chirality : 0.062 1.487 1277 Planarity : 0.005 0.057 1569 Dihedral : 8.826 84.204 1287 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.30 % Allowed : 21.56 % Favored : 73.14 % 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: 0.28 (0.26), residues: 1083 helix: 1.64 (0.28), residues: 380 sheet: -1.19 (0.64), residues: 72 loop : -0.55 (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 0.019 0.001 PHE A 80 TYR 0.015 0.002 TYR A 271 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 304) hydrogen bonds : angle 4.94369 ( 849) metal coordination : bond 0.00411 ( 3) metal coordination : angle 35.94684 ( 9) covalent geometry : bond 0.00514 ( 8839) covalent geometry : angle 1.08023 (12083) Misc. bond : bond 0.05231 ( 12) *********************** 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 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: A 84 ASN cc_start: 0.9083 (t0) cc_final: 0.8827 (t0) REVERT: A 156 MET cc_start: 0.8720 (mtp) cc_final: 0.8295 (mtp) REVERT: A 175 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.6868 (mmt) REVERT: A 221 ASN cc_start: 0.8590 (t0) cc_final: 0.7741 (t0) REVERT: A 247 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7780 (tttm) REVERT: A 266 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 305 ARG cc_start: 0.8632 (tpt90) cc_final: 0.7572 (ttm110) REVERT: A 308 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7703 (t-170) REVERT: A 535 ASP cc_start: 0.8618 (t0) cc_final: 0.8169 (m-30) REVERT: B 49 ASP cc_start: 0.8415 (m-30) cc_final: 0.8090 (t0) REVERT: B 100 ASN cc_start: 0.8462 (t0) cc_final: 0.8240 (t0) REVERT: B 141 VAL cc_start: 0.8736 (t) cc_final: 0.8506 (p) REVERT: B 173 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8553 (mm-30) REVERT: C 118 MET cc_start: 0.8768 (tpt) cc_final: 0.7828 (tpt) REVERT: C 161 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.7838 (ttm170) REVERT: C 211 LEU cc_start: 0.9386 (tp) cc_final: 0.8978 (tt) REVERT: C 328 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8421 (p) REVERT: C 394 LEU cc_start: 0.8441 (tp) cc_final: 0.8239 (tp) REVERT: C 395 MET cc_start: 0.8450 (tpt) cc_final: 0.8060 (tpt) outliers start: 47 outliers final: 30 residues processed: 150 average time/residue: 0.2026 time to fit residues: 42.9719 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 308 HIS 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 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 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** A 505 ASN 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 = 0.3317 r_free = 0.3317 target = 0.091159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073885 restraints weight = 17410.380| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.00 r_work: 0.2901 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 8854 Z= 0.142 Angle : 1.404 83.618 12092 Z= 0.409 Chirality : 0.060 1.469 1277 Planarity : 0.005 0.056 1569 Dihedral : 8.488 85.658 1287 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.51 % Allowed : 22.57 % Favored : 72.91 % 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: 0.29 (0.26), residues: 1083 helix: 1.66 (0.28), residues: 382 sheet: -1.34 (0.63), residues: 74 loop : -0.53 (0.25), residues: 627 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 0.006 0.000 ARG C 60 Details of bonding type rmsd hydrogen bonds : bond 0.02743 ( 304) hydrogen bonds : angle 4.73893 ( 849) metal coordination : bond 0.00281 ( 3) metal coordination : angle 34.47362 ( 9) covalent geometry : bond 0.00336 ( 8839) covalent geometry : angle 1.04327 (12083) Misc. bond : bond 0.03355 ( 12) *********************** 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 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.9012 (t0) cc_final: 0.8693 (t0) REVERT: A 156 MET cc_start: 0.8617 (mtp) cc_final: 0.8247 (mtp) REVERT: A 175 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7145 (mmt) REVERT: A 221 ASN cc_start: 0.8554 (t0) cc_final: 0.7635 (t0) REVERT: A 247 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7693 (tttm) REVERT: A 305 ARG cc_start: 0.8657 (tpt90) cc_final: 0.7590 (ttm110) REVERT: A 535 ASP cc_start: 0.8541 (t0) cc_final: 0.8130 (m-30) REVERT: B 49 ASP cc_start: 0.8404 (m-30) cc_final: 0.8061 (t0) REVERT: B 100 ASN cc_start: 0.8436 (t0) cc_final: 0.8234 (t0) REVERT: B 136 GLU cc_start: 0.9114 (pm20) cc_final: 0.8838 (pm20) REVERT: B 141 VAL cc_start: 0.8609 (t) cc_final: 0.8377 (p) REVERT: B 173 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8620 (mm-30) REVERT: B 177 VAL cc_start: 0.8866 (m) cc_final: 0.8609 (t) REVERT: C 118 MET cc_start: 0.8761 (tpt) cc_final: 0.7924 (tpt) REVERT: C 328 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8383 (p) REVERT: C 394 LEU cc_start: 0.8297 (tp) cc_final: 0.8055 (tp) REVERT: C 395 MET cc_start: 0.8205 (tpt) cc_final: 0.7802 (tpt) outliers start: 40 outliers final: 33 residues processed: 162 average time/residue: 0.1801 time to fit residues: 41.7607 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 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 73 SER Chi-restraints excluded: chain B residue 76 LEU 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 Chi-restraints excluded: chain C residue 411 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** A 505 ASN 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 = 0.090888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.071805 restraints weight = 18333.677| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.09 r_work: 0.2849 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 8854 Z= 0.180 Angle : 1.426 83.803 12092 Z= 0.417 Chirality : 0.061 1.479 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.627 86.363 1287 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.97 % Allowed : 22.12 % Favored : 72.91 % 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 (0.27), residues: 1083 helix: 1.68 (0.28), residues: 382 sheet: -1.53 (0.58), residues: 84 loop : -0.47 (0.26), residues: 617 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 0.027 0.001 TYR A 79 ARG 0.004 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 304) hydrogen bonds : angle 4.76517 ( 849) metal coordination : bond 0.00341 ( 3) metal coordination : angle 34.99801 ( 9) covalent geometry : bond 0.00435 ( 8839) covalent geometry : angle 1.05901 (12083) Misc. bond : bond 0.03931 ( 12) *********************** 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 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.072 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: 0.9007 (t0) cc_final: 0.8690 (t0) REVERT: A 156 MET cc_start: 0.8691 (mtp) cc_final: 0.8282 (mtp) REVERT: A 175 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7040 (mmt) REVERT: A 221 ASN cc_start: 0.8594 (t0) cc_final: 0.7677 (t0) REVERT: A 247 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7769 (tttm) REVERT: A 305 ARG cc_start: 0.8689 (tpt90) cc_final: 0.7516 (ttm110) REVERT: A 320 ASN cc_start: 0.7480 (t0) cc_final: 0.6991 (t0) REVERT: A 535 ASP cc_start: 0.8551 (t0) cc_final: 0.8130 (m-30) REVERT: B 49 ASP cc_start: 0.8396 (m-30) cc_final: 0.8075 (t70) REVERT: B 104 ASP cc_start: 0.8451 (m-30) cc_final: 0.7473 (p0) REVERT: B 136 GLU cc_start: 0.9093 (pm20) cc_final: 0.8792 (pm20) REVERT: B 141 VAL cc_start: 0.8685 (t) cc_final: 0.8454 (p) REVERT: B 173 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8679 (mm-30) REVERT: B 177 VAL cc_start: 0.8858 (m) cc_final: 0.8597 (t) REVERT: C 118 MET cc_start: 0.8748 (tpt) cc_final: 0.7879 (tpt) REVERT: C 328 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 394 LEU cc_start: 0.8333 (tp) cc_final: 0.8101 (tp) outliers start: 44 outliers final: 34 residues processed: 154 average time/residue: 0.1803 time to fit residues: 40.2626 Evaluate side-chains 149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 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 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 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: 20.0000 chunk 85 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 100 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 = 0.3293 r_free = 0.3293 target = 0.089633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.072502 restraints weight = 18016.668| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.00 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: 0.8058 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 8854 Z= 0.154 Angle : 1.410 83.708 12092 Z= 0.412 Chirality : 0.060 1.470 1277 Planarity : 0.005 0.062 1569 Dihedral : 8.444 86.725 1285 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.29 % Allowed : 23.36 % 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: 0.39 (0.26), residues: 1083 helix: 1.84 (0.28), residues: 370 sheet: -1.34 (0.58), residues: 83 loop : -0.46 (0.25), residues: 630 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 0.019 0.001 PHE B 60 TYR 0.023 0.001 TYR A 79 ARG 0.004 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02774 ( 304) hydrogen bonds : angle 4.73304 ( 849) metal coordination : bond 0.00292 ( 3) metal coordination : angle 34.53133 ( 9) covalent geometry : bond 0.00368 ( 8839) covalent geometry : angle 1.04954 (12083) Misc. bond : bond 0.03511 ( 12) *********************** 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 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.120 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 84 ASN cc_start: 0.9005 (t0) cc_final: 0.8737 (t0) REVERT: A 156 MET cc_start: 0.8656 (mtp) cc_final: 0.8294 (mtp) REVERT: A 175 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7081 (mmt) REVERT: A 221 ASN cc_start: 0.8587 (t0) cc_final: 0.7647 (t0) REVERT: A 247 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7774 (tttm) REVERT: A 305 ARG cc_start: 0.8688 (tpt90) cc_final: 0.7542 (ttm110) REVERT: A 320 ASN cc_start: 0.7275 (t0) cc_final: 0.6814 (t0) REVERT: A 535 ASP cc_start: 0.8536 (t0) cc_final: 0.8129 (m-30) REVERT: B 49 ASP cc_start: 0.8376 (m-30) cc_final: 0.8070 (t70) REVERT: B 83 LYS cc_start: 0.6121 (ptmm) cc_final: 0.5889 (ptmm) REVERT: B 104 ASP cc_start: 0.8476 (m-30) cc_final: 0.7557 (p0) REVERT: B 123 GLN cc_start: 0.8523 (tt0) cc_final: 0.8265 (tt0) REVERT: B 136 GLU cc_start: 0.9099 (pm20) cc_final: 0.8810 (pm20) REVERT: B 141 VAL cc_start: 0.8649 (t) cc_final: 0.8412 (p) REVERT: B 173 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 177 VAL cc_start: 0.8878 (m) cc_final: 0.8633 (t) REVERT: C 118 MET cc_start: 0.8724 (tpt) cc_final: 0.7897 (tpt) REVERT: C 182 HIS cc_start: 0.9178 (m90) cc_final: 0.8950 (m-70) REVERT: C 315 TYR cc_start: 0.7802 (p90) cc_final: 0.7587 (p90) REVERT: C 328 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 394 LEU cc_start: 0.8232 (tp) cc_final: 0.7969 (tp) outliers start: 38 outliers final: 33 residues processed: 150 average time/residue: 0.1979 time to fit residues: 41.8382 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 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 B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU 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 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 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: 6.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.0170 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 0.0980 chunk 99 optimal weight: 0.0270 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 B 123 GLN ** 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 = 0.3343 r_free = 0.3343 target = 0.092571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075429 restraints weight = 17885.411| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.10 r_work: 0.2914 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8854 Z= 0.139 Angle : 1.388 83.552 12092 Z= 0.410 Chirality : 0.059 1.466 1277 Planarity : 0.005 0.056 1569 Dihedral : 8.245 87.128 1285 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.72 % Allowed : 24.27 % Favored : 72.01 % 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: 0.45 (0.26), residues: 1083 helix: 1.84 (0.28), residues: 370 sheet: -0.78 (0.70), residues: 63 loop : -0.50 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.007 0.001 HIS A 503 PHE 0.021 0.001 PHE B 60 TYR 0.017 0.001 TYR A 79 ARG 0.008 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 304) hydrogen bonds : angle 4.64979 ( 849) metal coordination : bond 0.00246 ( 3) metal coordination : angle 33.38681 ( 9) covalent geometry : bond 0.00327 ( 8839) covalent geometry : angle 1.04812 (12083) Misc. bond : bond 0.02874 ( 12) *********************** 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 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.030 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 84 ASN cc_start: 0.8904 (t0) cc_final: 0.8506 (t0) REVERT: A 156 MET cc_start: 0.8614 (mtp) cc_final: 0.8309 (mtp) REVERT: A 175 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7216 (mmt) REVERT: A 221 ASN cc_start: 0.8586 (t0) cc_final: 0.7658 (t0) REVERT: A 247 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7747 (tttm) REVERT: A 305 ARG cc_start: 0.8682 (tpt90) cc_final: 0.7516 (ttm110) REVERT: A 535 ASP cc_start: 0.8504 (t0) cc_final: 0.8141 (m-30) REVERT: B 49 ASP cc_start: 0.8385 (m-30) cc_final: 0.8073 (t70) REVERT: B 104 ASP cc_start: 0.8477 (m-30) cc_final: 0.7608 (p0) REVERT: B 123 GLN cc_start: 0.8543 (tt0) cc_final: 0.8308 (tt0) REVERT: B 136 GLU cc_start: 0.9108 (pm20) cc_final: 0.8819 (pm20) REVERT: B 141 VAL cc_start: 0.8590 (t) cc_final: 0.8349 (p) REVERT: B 173 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8753 (mm-30) REVERT: B 177 VAL cc_start: 0.8913 (m) cc_final: 0.8711 (t) REVERT: C 115 TYR cc_start: 0.7630 (m-80) cc_final: 0.7330 (m-80) REVERT: C 118 MET cc_start: 0.8602 (tpt) cc_final: 0.7857 (tpt) REVERT: C 182 HIS cc_start: 0.9216 (m90) cc_final: 0.8973 (m-70) REVERT: C 328 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8330 (p) REVERT: C 394 LEU cc_start: 0.8071 (tp) cc_final: 0.7796 (tp) outliers start: 33 outliers final: 26 residues processed: 161 average time/residue: 0.1873 time to fit residues: 42.9364 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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 508 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 76 LEU 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 C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 179 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** 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 = 0.3316 r_free = 0.3316 target = 0.090864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073734 restraints weight = 17989.127| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.06 r_work: 0.2901 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8854 Z= 0.155 Angle : 1.379 83.737 12092 Z= 0.414 Chirality : 0.060 1.466 1277 Planarity : 0.005 0.053 1569 Dihedral : 8.331 87.695 1285 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.84 % Allowed : 24.15 % Favored : 72.01 % 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: 0.51 (0.26), residues: 1083 helix: 1.92 (0.28), residues: 369 sheet: -1.15 (0.62), residues: 74 loop : -0.41 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.008 0.001 PHE A 80 TYR 0.021 0.001 TYR A 79 ARG 0.008 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 304) hydrogen bonds : angle 4.66113 ( 849) metal coordination : bond 0.00255 ( 3) metal coordination : angle 32.59526 ( 9) covalent geometry : bond 0.00372 ( 8839) covalent geometry : angle 1.05445 (12083) Misc. bond : bond 0.03152 ( 12) ********************** 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 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.960 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: 0.8882 (t0) cc_final: 0.8474 (t0) REVERT: A 156 MET cc_start: 0.8676 (mtp) cc_final: 0.8293 (mtp) REVERT: A 175 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7186 (mmt) REVERT: A 221 ASN cc_start: 0.8571 (t0) cc_final: 0.7629 (t0) REVERT: A 247 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7734 (tttm) REVERT: A 305 ARG cc_start: 0.8676 (tpt90) cc_final: 0.7490 (ttm110) REVERT: A 535 ASP cc_start: 0.8515 (t0) cc_final: 0.8142 (m-30) REVERT: B 49 ASP cc_start: 0.8348 (m-30) cc_final: 0.8034 (t70) REVERT: B 104 ASP cc_start: 0.8448 (m-30) cc_final: 0.7552 (p0) REVERT: B 123 GLN cc_start: 0.8539 (tt0) cc_final: 0.8305 (tt0) REVERT: B 136 GLU cc_start: 0.9103 (pm20) cc_final: 0.8822 (pm20) REVERT: B 141 VAL cc_start: 0.8682 (t) cc_final: 0.8457 (p) REVERT: B 173 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8751 (mm-30) REVERT: B 177 VAL cc_start: 0.8914 (m) cc_final: 0.8710 (t) REVERT: C 118 MET cc_start: 0.8664 (tpt) cc_final: 0.8121 (tpt) REVERT: C 182 HIS cc_start: 0.9192 (m90) cc_final: 0.8955 (m-70) REVERT: C 328 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 394 LEU cc_start: 0.8174 (tp) cc_final: 0.7896 (tp) REVERT: C 395 MET cc_start: 0.8081 (tpt) cc_final: 0.7719 (tpt) outliers start: 34 outliers final: 30 residues processed: 148 average time/residue: 0.1843 time to fit residues: 38.8106 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 494 VAL 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 120 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 75 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** 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 = 0.3334 r_free = 0.3334 target = 0.092025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074830 restraints weight = 17915.503| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.17 r_work: 0.2917 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8854 Z= 0.147 Angle : 1.381 83.591 12092 Z= 0.413 Chirality : 0.060 1.472 1277 Planarity : 0.005 0.055 1569 Dihedral : 8.252 88.027 1285 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.61 % Allowed : 24.60 % 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: 0.46 (0.26), residues: 1083 helix: 1.89 (0.28), residues: 370 sheet: -1.43 (0.57), residues: 88 loop : -0.38 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS A 110 PHE 0.020 0.001 PHE B 60 TYR 0.019 0.001 TYR A 79 ARG 0.007 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.02638 ( 304) hydrogen bonds : angle 4.65501 ( 849) metal coordination : bond 0.00262 ( 3) metal coordination : angle 32.85267 ( 9) covalent geometry : bond 0.00352 ( 8839) covalent geometry : angle 1.05109 (12083) Misc. bond : bond 0.02973 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3979.36 seconds wall clock time: 69 minutes 53.02 seconds (4193.02 seconds total)