Starting phenix.real_space_refine on Thu Feb 13 16:29:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjq_43291/02_2025/8vjq_43291.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 V 2 8.30 5 Br 2 7.06 5 S 14 5.16 5 C 5796 2.51 5 N 1522 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9132 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4558 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "B" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4558 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 552} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' BR': 1, ' CA': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' BR': 1, ' CA': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.20, per 1000 atoms: 0.46 Number of scatterers: 9132 At special positions: 0 Unit cell: (106.496, 93.184, 100.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 2 34.99 V 2 22.97 Ca 2 19.99 S 14 16.00 O 1794 8.00 N 1522 7.00 C 5796 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 13 sheets defined 49.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.131A pdb=" N TYR A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.082A pdb=" N PHE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.112A pdb=" N GLY A 131 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.504A pdb=" N VAL A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.447A pdb=" N GLU A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.577A pdb=" N ILE A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.216A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.942A pdb=" N PHE A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.525A pdb=" N ASP A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 402 removed outlier: 4.293A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 532 through 550 removed outlier: 3.648A pdb=" N ARG A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 578 removed outlier: 3.885A pdb=" N LEU A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.988A pdb=" N TYR B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.695A pdb=" N ALA B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 154 through 170 removed outlier: 3.520A pdb=" N VAL B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 338 through 352 Processing helix chain 'B' and resid 377 through 402 removed outlier: 4.246A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 391 " --> pdb=" O GLU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 440 through 458 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 532 through 550 Processing helix chain 'B' and resid 554 through 580 removed outlier: 3.759A pdb=" N LEU B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 5.560A pdb=" N TRP A 125 " --> pdb=" O ASP B 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.741A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.741A pdb=" N THR A 279 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 279 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 286 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 318 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 7.136A pdb=" N VAL A 284 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY A 318 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.638A pdb=" N LEU A 530 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA9, first strand: chain 'A' and resid 586 through 589 Processing sheet with id=AB1, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.700A pdb=" N LEU B 530 " --> pdb=" O ILE B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 512 through 514 Processing sheet with id=AB4, first strand: chain 'B' and resid 586 through 589 414 hydrogen bonds defined for protein. 1200 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: 2.81 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1648 1.31 - 1.43: 2326 1.43 - 1.56: 5318 1.56 - 1.68: 6 1.68 - 1.80: 24 Bond restraints: 9322 Sorted by residual: bond pdb=" O1 VO4 B 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.549 0.361 2.00e-02 2.50e+03 3.25e+02 bond pdb=" O1 VO4 A 603 " pdb=" V VO4 A 603 " ideal model delta sigma weight residual 1.910 1.550 0.360 2.00e-02 2.50e+03 3.24e+02 bond pdb=" O2 VO4 B 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.571 0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" O2 VO4 A 603 " pdb=" V VO4 A 603 " ideal model delta sigma weight residual 1.910 1.573 0.337 2.00e-02 2.50e+03 2.84e+02 bond pdb=" O3 VO4 B 603 " pdb=" V VO4 B 603 " ideal model delta sigma weight residual 1.910 1.599 0.311 2.00e-02 2.50e+03 2.42e+02 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 12605 3.92 - 7.83: 50 7.83 - 11.75: 9 11.75 - 15.66: 4 15.66 - 19.58: 2 Bond angle restraints: 12670 Sorted by residual: angle pdb=" CA ASP B 335 " pdb=" CB ASP B 335 " pdb=" CG ASP B 335 " ideal model delta sigma weight residual 112.60 129.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " ideal model delta sigma weight residual 112.60 121.89 -9.29 1.00e+00 1.00e+00 8.64e+01 angle pdb=" CA PRO B 33 " pdb=" N PRO B 33 " pdb=" CD PRO B 33 " ideal model delta sigma weight residual 112.00 100.88 11.12 1.40e+00 5.10e-01 6.31e+01 angle pdb=" C ARG B 397 " pdb=" N TYR B 398 " pdb=" CA TYR B 398 " ideal model delta sigma weight residual 120.54 110.53 10.01 1.35e+00 5.49e-01 5.50e+01 angle pdb=" O ARG B 397 " pdb=" C ARG B 397 " pdb=" N TYR B 398 " ideal model delta sigma weight residual 122.23 131.45 -9.22 1.30e+00 5.92e-01 5.03e+01 ... (remaining 12665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4796 17.80 - 35.61: 604 35.61 - 53.41: 142 53.41 - 71.22: 38 71.22 - 89.02: 10 Dihedral angle restraints: 5590 sinusoidal: 2210 harmonic: 3380 Sorted by residual: dihedral pdb=" C HIS B 487 " pdb=" N HIS B 487 " pdb=" CA HIS B 487 " pdb=" CB HIS B 487 " ideal model delta harmonic sigma weight residual -122.60 -109.28 -13.32 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" C ARG A 397 " pdb=" N ARG A 397 " pdb=" CA ARG A 397 " pdb=" CB ARG A 397 " ideal model delta harmonic sigma weight residual -122.60 -112.84 -9.76 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA LEU B 337 " pdb=" C LEU B 337 " pdb=" N TYR B 338 " pdb=" CA TYR B 338 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1126 0.050 - 0.100: 239 0.100 - 0.151: 34 0.151 - 0.201: 1 0.201 - 0.251: 4 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB THR A 96 " pdb=" CA THR A 96 " pdb=" OG1 THR A 96 " pdb=" CG2 THR A 96 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASP A 335 " pdb=" N ASP A 335 " pdb=" C ASP A 335 " pdb=" CB ASP A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ARG A 397 " pdb=" N ARG A 397 " pdb=" C ARG A 397 " pdb=" CB ARG A 397 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1401 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 32 " 0.090 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO B 33 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 33 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 33 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 288 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 289 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 334 " 0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C PHE A 334 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 334 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP A 335 " 0.026 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 917 2.74 - 3.28: 10181 3.28 - 3.82: 17699 3.82 - 4.36: 22248 4.36 - 4.90: 36209 Nonbonded interactions: 87254 Sorted by model distance: nonbonded pdb=" NH1 ARG A 408 " pdb=" O VAL A 552 " model vdw 2.198 3.120 nonbonded pdb=" NH2 ARG A 29 " pdb=" OE2 GLU A 575 " model vdw 2.222 3.120 nonbonded pdb=" CE2 TYR A 341 " pdb=" O HOH A 701 " model vdw 2.224 3.340 nonbonded pdb=" NH1 ARG A 406 " pdb=" OD1 ASP A 557 " model vdw 2.226 3.120 nonbonded pdb=" NH2 ARG B 29 " pdb=" OE2 GLU B 575 " model vdw 2.226 3.120 ... (remaining 87249 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 16.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.010 0.361 9322 Z= 0.741 Angle : 0.811 19.579 12670 Z= 0.475 Chirality : 0.043 0.251 1404 Planarity : 0.009 0.128 1702 Dihedral : 17.114 89.022 3414 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.31 % Allowed : 23.87 % Favored : 75.82 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.02 (0.24), residues: 1176 helix: 0.43 (0.22), residues: 528 sheet: -1.41 (1.35), residues: 18 loop : -0.25 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 110 HIS 0.021 0.002 HIS B 487 PHE 0.016 0.001 PHE A 376 TYR 0.048 0.003 TYR B 341 ARG 0.018 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.882 Fit side-chains REVERT: B 515 ASP cc_start: 0.7847 (t0) cc_final: 0.7531 (m-30) REVERT: B 592 ASP cc_start: 0.8285 (p0) cc_final: 0.8037 (p0) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.2174 time to fit residues: 36.0583 Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 304 GLN A 419 ASN A 542 ASN B 68 ASN B 183 ASN B 224 ASN B 351 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125784 restraints weight = 8871.858| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.14 r_work: 0.3192 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9322 Z= 0.258 Angle : 0.571 6.545 12670 Z= 0.293 Chirality : 0.041 0.171 1404 Planarity : 0.006 0.068 1702 Dihedral : 4.396 41.185 1262 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.60 % Allowed : 21.50 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.49 (0.24), residues: 1176 helix: 0.95 (0.22), residues: 518 sheet: -1.87 (1.19), residues: 18 loop : -0.03 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 199 HIS 0.008 0.002 HIS A 487 PHE 0.014 0.001 PHE A 479 TYR 0.033 0.003 TYR A 341 ARG 0.008 0.001 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.971 Fit side-chains REVERT: A 243 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 364 GLU cc_start: 0.7562 (tp30) cc_final: 0.6921 (tt0) REVERT: A 501 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7833 (t80) REVERT: B 173 ILE cc_start: 0.8464 (mm) cc_final: 0.7984 (mm) REVERT: B 183 ASN cc_start: 0.6982 (m-40) cc_final: 0.6548 (m110) REVERT: B 254 THR cc_start: 0.8694 (t) cc_final: 0.8469 (t) REVERT: B 438 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 592 ASP cc_start: 0.8286 (p0) cc_final: 0.8032 (p0) outliers start: 35 outliers final: 18 residues processed: 155 average time/residue: 0.2152 time to fit residues: 47.3636 Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 471 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125657 restraints weight = 8965.261| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.18 r_work: 0.3136 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9322 Z= 0.264 Angle : 0.554 6.339 12670 Z= 0.282 Chirality : 0.041 0.172 1404 Planarity : 0.005 0.053 1702 Dihedral : 4.339 42.151 1262 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.91 % Allowed : 21.71 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.61 (0.24), residues: 1176 helix: 1.02 (0.22), residues: 520 sheet: -1.93 (1.09), residues: 18 loop : 0.06 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 199 HIS 0.007 0.002 HIS A 487 PHE 0.014 0.001 PHE A 479 TYR 0.032 0.003 TYR B 341 ARG 0.005 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.948 Fit side-chains REVERT: A 63 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8381 (mt) REVERT: A 243 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 364 GLU cc_start: 0.7636 (tp30) cc_final: 0.6932 (tt0) REVERT: A 566 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: B 173 ILE cc_start: 0.8427 (mm) cc_final: 0.7933 (mm) REVERT: B 183 ASN cc_start: 0.6916 (m-40) cc_final: 0.6210 (m110) REVERT: B 297 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.6971 (mt) REVERT: B 438 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6875 (mt-10) REVERT: B 592 ASP cc_start: 0.8143 (p0) cc_final: 0.7841 (p0) outliers start: 38 outliers final: 21 residues processed: 146 average time/residue: 0.2100 time to fit residues: 43.8325 Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 471 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.0040 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 127 ASN B 224 ASN ** B 362 GLN ** 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 = 0.3551 r_free = 0.3551 target = 0.144842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.128782 restraints weight = 8823.475| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.38 r_work: 0.3193 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.032 9322 Z= 0.224 Angle : 0.536 6.153 12670 Z= 0.270 Chirality : 0.040 0.145 1404 Planarity : 0.005 0.054 1702 Dihedral : 4.281 42.840 1262 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.73 % Allowed : 20.88 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1176 helix: 1.11 (0.22), residues: 520 sheet: -2.21 (0.99), residues: 18 loop : 0.16 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.006 0.001 HIS A 487 PHE 0.011 0.001 PHE A 376 TYR 0.030 0.003 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 1.027 Fit side-chains REVERT: A 243 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 364 GLU cc_start: 0.7517 (tp30) cc_final: 0.6780 (tt0) REVERT: A 471 MET cc_start: 0.8122 (mtp) cc_final: 0.7574 (mtp) REVERT: A 501 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7837 (t80) REVERT: A 566 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 173 ILE cc_start: 0.8344 (mm) cc_final: 0.7820 (mm) REVERT: B 183 ASN cc_start: 0.6972 (m-40) cc_final: 0.6238 (m110) REVERT: B 254 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8270 (t) REVERT: B 297 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.6890 (mt) REVERT: B 438 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6789 (mt-10) REVERT: B 515 ASP cc_start: 0.8262 (t0) cc_final: 0.7897 (m-30) REVERT: B 522 VAL cc_start: 0.8329 (m) cc_final: 0.8120 (m) REVERT: B 548 ASN cc_start: 0.8171 (m-40) cc_final: 0.7925 (m-40) REVERT: B 592 ASP cc_start: 0.8139 (p0) cc_final: 0.7892 (p0) outliers start: 46 outliers final: 29 residues processed: 154 average time/residue: 0.1880 time to fit residues: 42.5639 Evaluate side-chains 144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 116 optimal weight: 0.3980 chunk 58 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 542 ASN B 224 ASN B 358 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.144033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.128699 restraints weight = 8925.898| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.31 r_work: 0.3199 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9322 Z= 0.206 Angle : 0.527 6.019 12670 Z= 0.267 Chirality : 0.040 0.142 1404 Planarity : 0.004 0.055 1702 Dihedral : 4.240 43.343 1262 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.53 % Allowed : 21.30 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.84 (0.25), residues: 1176 helix: 1.22 (0.22), residues: 520 sheet: -2.51 (0.91), residues: 18 loop : 0.21 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.010 0.001 PHE A 376 TYR 0.029 0.002 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.938 Fit side-chains REVERT: A 68 ASN cc_start: 0.8433 (m110) cc_final: 0.8142 (m-40) REVERT: A 243 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 364 GLU cc_start: 0.7590 (tp30) cc_final: 0.6885 (tt0) REVERT: A 501 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7902 (t80) REVERT: A 566 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: B 254 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8353 (t) REVERT: B 297 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.6940 (mt) REVERT: B 438 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6834 (mt-10) REVERT: B 501 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 515 ASP cc_start: 0.8285 (t0) cc_final: 0.7964 (m-30) REVERT: B 522 VAL cc_start: 0.8361 (m) cc_final: 0.8122 (m) REVERT: B 542 ASN cc_start: 0.8498 (m110) cc_final: 0.8205 (m-40) REVERT: B 592 ASP cc_start: 0.8087 (p0) cc_final: 0.7834 (p0) outliers start: 44 outliers final: 29 residues processed: 156 average time/residue: 0.1894 time to fit residues: 43.4646 Evaluate side-chains 140 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS B 68 ASN B 127 ASN B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130757 restraints weight = 8751.189| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.38 r_work: 0.3195 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9322 Z= 0.201 Angle : 0.526 5.974 12670 Z= 0.266 Chirality : 0.040 0.178 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.225 44.165 1262 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.84 % Allowed : 21.30 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.91 (0.25), residues: 1176 helix: 1.29 (0.22), residues: 520 sheet: -2.66 (0.87), residues: 18 loop : 0.23 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.014 0.001 PHE B 376 TYR 0.029 0.002 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.952 Fit side-chains REVERT: A 68 ASN cc_start: 0.8500 (m110) cc_final: 0.8104 (m-40) REVERT: A 127 ASN cc_start: 0.8494 (m110) cc_final: 0.8290 (m110) REVERT: A 243 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8461 (tt) REVERT: A 364 GLU cc_start: 0.7476 (tp30) cc_final: 0.6772 (tt0) REVERT: A 501 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 566 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: B 254 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 438 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6726 (mm-30) REVERT: B 480 HIS cc_start: 0.9203 (OUTLIER) cc_final: 0.8932 (p90) REVERT: B 501 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: B 515 ASP cc_start: 0.8233 (t0) cc_final: 0.7909 (m-30) REVERT: B 522 VAL cc_start: 0.8303 (m) cc_final: 0.8086 (m) REVERT: B 542 ASN cc_start: 0.8500 (m110) cc_final: 0.8181 (m-40) REVERT: B 592 ASP cc_start: 0.8067 (p0) cc_final: 0.7801 (p0) outliers start: 47 outliers final: 29 residues processed: 156 average time/residue: 0.1844 time to fit residues: 42.8042 Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 0.0040 chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 224 ASN B 304 GLN ** B 362 GLN ** 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 = 0.3568 r_free = 0.3568 target = 0.146244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130471 restraints weight = 8902.392| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.36 r_work: 0.3189 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9322 Z= 0.224 Angle : 0.540 7.659 12670 Z= 0.272 Chirality : 0.040 0.222 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.233 44.525 1262 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.63 % Allowed : 21.60 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.97 (0.25), residues: 1176 helix: 1.31 (0.23), residues: 512 sheet: -2.77 (0.82), residues: 18 loop : 0.32 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.012 0.001 PHE B 376 TYR 0.030 0.002 TYR B 341 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.963 Fit side-chains REVERT: A 68 ASN cc_start: 0.8514 (m110) cc_final: 0.8115 (m-40) REVERT: A 243 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8387 (tt) REVERT: A 501 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 566 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: B 13 LYS cc_start: 0.7917 (tptp) cc_final: 0.7691 (tptt) REVERT: B 254 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8329 (t) REVERT: B 438 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6760 (mm-30) REVERT: B 480 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8939 (p90) REVERT: B 501 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 515 ASP cc_start: 0.8135 (t0) cc_final: 0.7806 (m-30) REVERT: B 522 VAL cc_start: 0.8368 (m) cc_final: 0.8145 (m) REVERT: B 592 ASP cc_start: 0.8047 (p0) cc_final: 0.7801 (p0) outliers start: 45 outliers final: 33 residues processed: 153 average time/residue: 0.1942 time to fit residues: 44.0497 Evaluate side-chains 151 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 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 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 127 ASN B 224 ASN ** B 362 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.125322 restraints weight = 9087.339| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.36 r_work: 0.3228 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9322 Z= 0.264 Angle : 0.555 7.530 12670 Z= 0.280 Chirality : 0.041 0.214 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.277 44.859 1262 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.73 % Allowed : 21.71 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.88 (0.25), residues: 1176 helix: 1.19 (0.22), residues: 514 sheet: -2.76 (0.80), residues: 18 loop : 0.32 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.011 0.001 PHE B 501 TYR 0.031 0.003 TYR B 341 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.994 Fit side-chains REVERT: A 68 ASN cc_start: 0.8522 (m110) cc_final: 0.8132 (m-40) REVERT: A 102 ASP cc_start: 0.7522 (t0) cc_final: 0.7093 (t0) REVERT: A 137 GLU cc_start: 0.7847 (mp0) cc_final: 0.7384 (mp0) REVERT: A 243 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 501 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 566 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: B 254 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8364 (t) REVERT: B 297 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.6904 (mt) REVERT: B 438 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6783 (mm-30) REVERT: B 501 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: B 515 ASP cc_start: 0.8154 (t0) cc_final: 0.7819 (m-30) REVERT: B 592 ASP cc_start: 0.8075 (p0) cc_final: 0.7825 (p0) outliers start: 46 outliers final: 32 residues processed: 146 average time/residue: 0.1835 time to fit residues: 39.5772 Evaluate side-chains 145 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 68 ASN B 224 ASN ** B 362 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.141204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.125365 restraints weight = 8921.125| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.34 r_work: 0.3162 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9322 Z= 0.259 Angle : 0.556 7.352 12670 Z= 0.281 Chirality : 0.041 0.198 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.304 45.216 1262 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.63 % Allowed : 21.91 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.88 (0.25), residues: 1176 helix: 1.18 (0.22), residues: 512 sheet: -2.82 (0.79), residues: 18 loop : 0.32 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.011 0.001 PHE B 501 TYR 0.030 0.003 TYR B 341 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.947 Fit side-chains REVERT: A 68 ASN cc_start: 0.8484 (m110) cc_final: 0.8111 (m-40) REVERT: A 102 ASP cc_start: 0.7519 (t0) cc_final: 0.7093 (t0) REVERT: A 137 GLU cc_start: 0.7847 (mp0) cc_final: 0.7381 (mp0) REVERT: A 243 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 501 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7998 (t80) REVERT: A 566 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: B 137 GLU cc_start: 0.8059 (tt0) cc_final: 0.7824 (tt0) REVERT: B 254 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8374 (t) REVERT: B 297 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.6878 (mt) REVERT: B 438 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6780 (mm-30) REVERT: B 480 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (p90) REVERT: B 501 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 515 ASP cc_start: 0.8142 (t0) cc_final: 0.7814 (m-30) REVERT: B 592 ASP cc_start: 0.7987 (p0) cc_final: 0.7700 (p0) outliers start: 45 outliers final: 33 residues processed: 150 average time/residue: 0.1760 time to fit residues: 39.2348 Evaluate side-chains 150 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.127731 restraints weight = 8939.282| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.40 r_work: 0.3161 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9322 Z= 0.243 Angle : 0.561 7.208 12670 Z= 0.282 Chirality : 0.041 0.196 1404 Planarity : 0.005 0.061 1702 Dihedral : 4.313 45.736 1262 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.53 % Allowed : 22.43 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.90 (0.25), residues: 1176 helix: 1.19 (0.22), residues: 512 sheet: -2.95 (0.77), residues: 18 loop : 0.34 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.011 0.001 PHE B 501 TYR 0.031 0.003 TYR B 341 ARG 0.006 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.871 Fit side-chains REVERT: A 68 ASN cc_start: 0.8471 (m110) cc_final: 0.8178 (m-40) REVERT: A 102 ASP cc_start: 0.7503 (t0) cc_final: 0.7094 (t0) REVERT: A 137 GLU cc_start: 0.7841 (mp0) cc_final: 0.7347 (mp0) REVERT: A 243 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 501 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 566 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: B 137 GLU cc_start: 0.8038 (tt0) cc_final: 0.7803 (tt0) REVERT: B 254 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 438 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6722 (mm-30) REVERT: B 480 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8951 (p90) REVERT: B 501 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: B 515 ASP cc_start: 0.8164 (t0) cc_final: 0.7837 (m-30) REVERT: B 592 ASP cc_start: 0.7980 (p0) cc_final: 0.7732 (p0) outliers start: 44 outliers final: 34 residues processed: 145 average time/residue: 0.1811 time to fit residues: 39.1208 Evaluate side-chains 146 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 479 PHE Chi-restraints excluded: chain B residue 480 HIS Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 535 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 68 ASN B 224 ASN ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.143114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.127501 restraints weight = 8920.580| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.32 r_work: 0.3202 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9322 Z= 0.238 Angle : 0.560 7.106 12670 Z= 0.282 Chirality : 0.041 0.193 1404 Planarity : 0.005 0.055 1702 Dihedral : 4.318 46.205 1262 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.63 % Allowed : 22.22 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.91 (0.25), residues: 1176 helix: 1.21 (0.22), residues: 512 sheet: -3.07 (0.74), residues: 18 loop : 0.34 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 331 HIS 0.005 0.001 HIS A 487 PHE 0.011 0.001 PHE B 501 TYR 0.031 0.003 TYR B 341 ARG 0.006 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4734.30 seconds wall clock time: 86 minutes 6.38 seconds (5166.38 seconds total)