Starting phenix.real_space_refine on Sat Aug 23 04:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tok_41454/08_2025/8tok_41454.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 40 5.16 5 C 6494 2.51 5 N 1648 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4952 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 599} Chain breaks: 6 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 3.05, per 1000 atoms: 0.31 Number of scatterers: 9908 At special positions: 0 Unit cell: (128.31, 104.65, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 40 16.00 O 1722 8.00 N 1648 7.00 C 6494 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=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 252.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 73.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 72 through 91 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.025A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.960A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.959A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.522A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.924A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 4.047A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 330 through 357 Proline residue: A 341 - end of helix removed outlier: 3.870A pdb=" N MET A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 4.120A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 Processing helix chain 'A' and resid 431 through 466 removed outlier: 4.440A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.775A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.749A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 removed outlier: 3.527A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.524A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 4.039A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 72 through 91 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 135 through 139 removed outlier: 4.023A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.960A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.959A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.521A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.924A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 4.047A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 330 through 357 Proline residue: B 341 - end of helix removed outlier: 3.869A pdb=" N MET B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 4.120A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 416 Processing helix chain 'B' and resid 431 through 466 removed outlier: 4.440A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 482 through 495 Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.773A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.749A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.527A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.524A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 4.039A pdb=" N LEU B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 701 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.966A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.967A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2016 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: 1.27 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3095 1.34 - 1.46: 2464 1.46 - 1.58: 4547 1.58 - 1.70: 4 1.70 - 1.81: 66 Bond restraints: 10176 Sorted by residual: bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.647 -0.155 5.00e-02 4.00e+02 9.57e+00 bond pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.44e+00 bond pdb=" CB PRO A 596 " pdb=" CG PRO A 596 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.20e+00 bond pdb=" CB PRO B 596 " pdb=" CG PRO B 596 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.17e+00 bond pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.64e+00 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 13800 3.41 - 6.83: 36 6.83 - 10.24: 8 10.24 - 13.66: 2 13.66 - 17.07: 2 Bond angle restraints: 13848 Sorted by residual: angle pdb=" CA PRO B 202 " pdb=" N PRO B 202 " pdb=" CD PRO B 202 " ideal model delta sigma weight residual 112.00 94.93 17.07 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO A 202 " pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 112.00 94.99 17.01 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO A 202 " pdb=" CD PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 103.20 95.15 8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" N PRO B 202 " pdb=" CD PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 103.20 95.18 8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" CA PRO B 596 " pdb=" N PRO B 596 " pdb=" CD PRO B 596 " ideal model delta sigma weight residual 112.00 107.00 5.00 1.40e+00 5.10e-01 1.28e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4932 17.12 - 34.23: 736 34.23 - 51.35: 203 51.35 - 68.46: 27 68.46 - 85.58: 12 Dihedral angle restraints: 5910 sinusoidal: 2240 harmonic: 3670 Sorted by residual: dihedral pdb=" CA VAL A 453 " pdb=" C VAL A 453 " pdb=" N VAL A 454 " pdb=" CA VAL A 454 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA VAL B 453 " pdb=" C VAL B 453 " pdb=" N VAL B 454 " pdb=" CA VAL B 454 " ideal model delta harmonic sigma weight residual 180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CG ARG A 548 " pdb=" CD ARG A 548 " pdb=" NE ARG A 548 " pdb=" CZ ARG A 548 " ideal model delta sinusoidal sigma weight residual -90.00 -133.76 43.76 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1091 0.031 - 0.061: 309 0.061 - 0.092: 94 0.092 - 0.123: 48 0.123 - 0.154: 10 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA PRO B 402 " pdb=" N PRO B 402 " pdb=" C PRO B 402 " pdb=" CB PRO B 402 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1549 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 201 " 0.096 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO A 202 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 201 " -0.096 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO B 202 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 402 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.038 5.00e-02 4.00e+02 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 537 2.74 - 3.28: 9826 3.28 - 3.82: 16631 3.82 - 4.36: 16220 4.36 - 4.90: 30638 Nonbonded interactions: 73852 Sorted by model distance: nonbonded pdb=" O SER A 165 " pdb=" OG SER A 165 " model vdw 2.195 3.040 nonbonded pdb=" O SER B 165 " pdb=" OG SER B 165 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.236 3.040 nonbonded pdb=" O TRP A 407 " pdb=" OG1 THR A 410 " model vdw 2.271 3.040 ... (remaining 73847 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: 0.01 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.004 0.155 10176 Z= 0.133 Angle : 0.602 17.072 13848 Z= 0.337 Chirality : 0.037 0.154 1552 Planarity : 0.006 0.132 1738 Dihedral : 17.557 85.575 3526 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 29.63 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.24), residues: 1230 helix: 2.60 (0.17), residues: 832 sheet: -2.23 (0.79), residues: 48 loop : -1.77 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 249 TYR 0.006 0.001 TYR B 26 PHE 0.033 0.001 PHE B 315 TRP 0.012 0.001 TRP A 521 HIS 0.003 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00356 (10176) covalent geometry : angle 0.60191 (13848) hydrogen bonds : bond 0.13969 ( 682) hydrogen bonds : angle 4.75697 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0733 time to fit residues: 10.0777 Evaluate side-chains 87 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 445 GLN A 611 HIS B 79 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS B 445 GLN B 611 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113151 restraints weight = 13392.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112146 restraints weight = 20406.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112929 restraints weight = 18221.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112531 restraints weight = 14590.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112752 restraints weight = 13569.437| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10176 Z= 0.147 Angle : 0.539 10.171 13848 Z= 0.279 Chirality : 0.039 0.154 1552 Planarity : 0.004 0.063 1738 Dihedral : 3.580 19.261 1340 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.85 % Allowed : 29.82 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.25), residues: 1230 helix: 2.81 (0.17), residues: 862 sheet: -1.36 (0.68), residues: 68 loop : -2.28 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 621 TYR 0.010 0.001 TYR A 26 PHE 0.014 0.001 PHE B 379 TRP 0.011 0.001 TRP A 533 HIS 0.003 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00348 (10176) covalent geometry : angle 0.53936 (13848) hydrogen bonds : bond 0.05047 ( 682) hydrogen bonds : angle 3.58126 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.373 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 119 average time/residue: 0.0843 time to fit residues: 14.8818 Evaluate side-chains 106 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 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 = 0.3550 r_free = 0.3550 target = 0.143329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114283 restraints weight = 13406.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112808 restraints weight = 17901.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113738 restraints weight = 17345.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113985 restraints weight = 13460.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114220 restraints weight = 12557.761| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10176 Z= 0.134 Angle : 0.526 9.387 13848 Z= 0.269 Chirality : 0.038 0.150 1552 Planarity : 0.004 0.051 1738 Dihedral : 3.544 19.560 1340 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.15 % Allowed : 30.41 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.25), residues: 1230 helix: 2.77 (0.17), residues: 874 sheet: -1.47 (0.66), residues: 68 loop : -2.30 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.010 0.001 TYR B 26 PHE 0.013 0.001 PHE B 379 TRP 0.010 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00316 (10176) covalent geometry : angle 0.52573 (13848) hydrogen bonds : bond 0.04889 ( 682) hydrogen bonds : angle 3.44089 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.347 Fit side-chains REVERT: A 175 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: A 219 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 48 THR cc_start: 0.8036 (m) cc_final: 0.7829 (m) REVERT: B 122 MET cc_start: 0.8689 (ttm) cc_final: 0.8287 (ttm) REVERT: B 219 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7716 (tt) outliers start: 32 outliers final: 22 residues processed: 121 average time/residue: 0.0811 time to fit residues: 14.7873 Evaluate side-chains 117 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 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 = 0.3528 r_free = 0.3528 target = 0.141623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111496 restraints weight = 13530.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111117 restraints weight = 17188.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112194 restraints weight = 14530.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112099 restraints weight = 11942.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112339 restraints weight = 11155.070| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10176 Z= 0.150 Angle : 0.542 8.805 13848 Z= 0.276 Chirality : 0.039 0.147 1552 Planarity : 0.004 0.045 1738 Dihedral : 3.565 19.578 1340 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.94 % Allowed : 30.51 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.25), residues: 1230 helix: 2.69 (0.17), residues: 874 sheet: -1.46 (0.64), residues: 68 loop : -2.37 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.011 0.001 TYR A 26 PHE 0.018 0.001 PHE A 379 TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00359 (10176) covalent geometry : angle 0.54216 (13848) hydrogen bonds : bond 0.05211 ( 682) hydrogen bonds : angle 3.42301 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.374 Fit side-chains REVERT: A 122 MET cc_start: 0.8710 (ttm) cc_final: 0.8284 (ttm) REVERT: A 219 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7846 (tt) REVERT: B 122 MET cc_start: 0.8722 (ttm) cc_final: 0.8297 (ttm) REVERT: B 219 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7848 (tt) outliers start: 40 outliers final: 31 residues processed: 123 average time/residue: 0.0915 time to fit residues: 16.8129 Evaluate side-chains 118 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110258 restraints weight = 13693.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108826 restraints weight = 15187.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109549 restraints weight = 13794.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109747 restraints weight = 11527.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109980 restraints weight = 10340.704| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10176 Z= 0.159 Angle : 0.560 8.302 13848 Z= 0.289 Chirality : 0.039 0.167 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.613 19.195 1340 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.92 % Allowed : 28.94 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.25), residues: 1230 helix: 2.62 (0.17), residues: 874 sheet: -1.58 (0.64), residues: 68 loop : -2.40 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.011 0.001 TYR A 26 PHE 0.016 0.001 PHE A 379 TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00382 (10176) covalent geometry : angle 0.56001 (13848) hydrogen bonds : bond 0.05367 ( 682) hydrogen bonds : angle 3.41561 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 0.293 Fit side-chains REVERT: A 219 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 521 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7280 (t60) REVERT: B 122 MET cc_start: 0.8711 (ttm) cc_final: 0.8263 (ttm) REVERT: B 219 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 521 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7284 (t60) outliers start: 50 outliers final: 41 residues processed: 130 average time/residue: 0.0838 time to fit residues: 16.6740 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110121 restraints weight = 13640.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109455 restraints weight = 17982.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110261 restraints weight = 15057.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110653 restraints weight = 11949.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110903 restraints weight = 10743.675| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10176 Z= 0.133 Angle : 0.529 7.795 13848 Z= 0.271 Chirality : 0.038 0.144 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.582 19.307 1340 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.84 % Allowed : 29.63 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.25), residues: 1230 helix: 2.69 (0.17), residues: 874 sheet: -2.22 (0.72), residues: 48 loop : -2.20 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 45 TYR 0.010 0.001 TYR B 26 PHE 0.019 0.001 PHE B 205 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00315 (10176) covalent geometry : angle 0.52891 (13848) hydrogen bonds : bond 0.04876 ( 682) hydrogen bonds : angle 3.31267 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.380 Fit side-chains REVERT: A 48 THR cc_start: 0.8274 (m) cc_final: 0.8025 (m) REVERT: A 122 MET cc_start: 0.8700 (ttm) cc_final: 0.8292 (ttm) REVERT: A 219 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 509 MET cc_start: 0.8335 (mmp) cc_final: 0.7950 (mmp) REVERT: A 521 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7274 (t60) REVERT: B 122 MET cc_start: 0.8695 (ttm) cc_final: 0.8258 (ttm) REVERT: B 219 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7838 (tt) REVERT: B 491 GLU cc_start: 0.6240 (tp30) cc_final: 0.6038 (tp30) REVERT: B 495 LEU cc_start: 0.7885 (mp) cc_final: 0.7580 (mp) REVERT: B 509 MET cc_start: 0.8331 (mmp) cc_final: 0.7932 (mmp) REVERT: B 521 TRP cc_start: 0.8167 (OUTLIER) cc_final: 0.7277 (t60) outliers start: 39 outliers final: 30 residues processed: 123 average time/residue: 0.0863 time to fit residues: 16.0933 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111006 restraints weight = 13633.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110428 restraints weight = 18312.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111310 restraints weight = 14915.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111525 restraints weight = 11854.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111631 restraints weight = 11434.449| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.125 Angle : 0.525 10.636 13848 Z= 0.267 Chirality : 0.038 0.142 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.536 19.232 1340 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.44 % Allowed : 30.02 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.25), residues: 1230 helix: 2.74 (0.17), residues: 874 sheet: -2.25 (0.73), residues: 48 loop : -2.19 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.010 0.001 TYR B 26 PHE 0.018 0.001 PHE A 205 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00294 (10176) covalent geometry : angle 0.52544 (13848) hydrogen bonds : bond 0.04611 ( 682) hydrogen bonds : angle 3.26066 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.378 Fit side-chains REVERT: A 75 LEU cc_start: 0.8255 (mt) cc_final: 0.7751 (tt) REVERT: A 122 MET cc_start: 0.8674 (ttm) cc_final: 0.8277 (ttm) REVERT: A 219 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 309 CYS cc_start: 0.7031 (m) cc_final: 0.6566 (m) REVERT: A 495 LEU cc_start: 0.7843 (mp) cc_final: 0.7438 (mp) REVERT: A 509 MET cc_start: 0.8274 (mmp) cc_final: 0.7934 (mmp) REVERT: A 521 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7260 (t60) REVERT: B 122 MET cc_start: 0.8670 (ttm) cc_final: 0.8237 (ttm) REVERT: B 219 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 491 GLU cc_start: 0.6227 (tp30) cc_final: 0.6017 (tp30) REVERT: B 495 LEU cc_start: 0.7815 (mp) cc_final: 0.7511 (mp) REVERT: B 509 MET cc_start: 0.8310 (mmp) cc_final: 0.7948 (mmp) REVERT: B 521 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7260 (t60) outliers start: 35 outliers final: 29 residues processed: 123 average time/residue: 0.0840 time to fit residues: 15.6577 Evaluate side-chains 119 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 22 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115549 restraints weight = 13440.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114487 restraints weight = 16725.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115639 restraints weight = 16091.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115943 restraints weight = 12082.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116095 restraints weight = 12126.049| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10176 Z= 0.107 Angle : 0.515 10.889 13848 Z= 0.257 Chirality : 0.037 0.142 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.467 19.009 1340 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.05 % Allowed : 29.92 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.25), residues: 1230 helix: 2.84 (0.17), residues: 874 sheet: -2.15 (0.74), residues: 48 loop : -2.14 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.009 0.001 TYR B 26 PHE 0.011 0.001 PHE B 205 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00244 (10176) covalent geometry : angle 0.51536 (13848) hydrogen bonds : bond 0.03940 ( 682) hydrogen bonds : angle 3.14702 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.384 Fit side-chains REVERT: A 75 LEU cc_start: 0.8244 (mt) cc_final: 0.7617 (tp) REVERT: A 122 MET cc_start: 0.8639 (ttm) cc_final: 0.8275 (ttm) REVERT: A 219 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7614 (tt) REVERT: A 309 CYS cc_start: 0.6970 (m) cc_final: 0.6467 (m) REVERT: A 491 GLU cc_start: 0.6319 (tp30) cc_final: 0.6105 (tp30) REVERT: A 495 LEU cc_start: 0.7690 (mp) cc_final: 0.7261 (mp) REVERT: A 509 MET cc_start: 0.8022 (mmp) cc_final: 0.7726 (mmp) REVERT: A 521 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7268 (t60) REVERT: B 75 LEU cc_start: 0.8232 (mt) cc_final: 0.7706 (tt) REVERT: B 122 MET cc_start: 0.8623 (ttm) cc_final: 0.8264 (ttm) REVERT: B 219 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7600 (tt) REVERT: B 309 CYS cc_start: 0.6985 (m) cc_final: 0.6529 (m) REVERT: B 491 GLU cc_start: 0.6208 (tp30) cc_final: 0.5994 (tp30) REVERT: B 495 LEU cc_start: 0.7686 (mp) cc_final: 0.7368 (mp) REVERT: B 509 MET cc_start: 0.8061 (mmp) cc_final: 0.7789 (mmp) REVERT: B 521 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.7268 (t60) outliers start: 31 outliers final: 24 residues processed: 122 average time/residue: 0.0828 time to fit residues: 15.3714 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108744 restraints weight = 13759.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107428 restraints weight = 22880.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107956 restraints weight = 20597.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108168 restraints weight = 15506.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108369 restraints weight = 14705.203| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10176 Z= 0.207 Angle : 0.604 10.551 13848 Z= 0.309 Chirality : 0.040 0.174 1552 Planarity : 0.004 0.029 1738 Dihedral : 3.622 19.245 1340 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.13 % Allowed : 29.23 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.25), residues: 1230 helix: 2.58 (0.17), residues: 874 sheet: -2.17 (0.72), residues: 48 loop : -2.21 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.011 0.001 TYR B 220 PHE 0.021 0.002 PHE B 205 TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00514 (10176) covalent geometry : angle 0.60421 (13848) hydrogen bonds : bond 0.05965 ( 682) hydrogen bonds : angle 3.44840 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.391 Fit side-chains REVERT: A 75 LEU cc_start: 0.8297 (mt) cc_final: 0.7870 (tt) REVERT: A 108 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: A 219 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 521 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7251 (t60) REVERT: A 605 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8378 (t) REVERT: B 75 LEU cc_start: 0.8244 (mt) cc_final: 0.7797 (tt) REVERT: B 122 MET cc_start: 0.8750 (ttm) cc_final: 0.8396 (ttm) REVERT: B 219 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 495 LEU cc_start: 0.8202 (mp) cc_final: 0.8000 (mt) REVERT: B 521 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7251 (t60) outliers start: 42 outliers final: 31 residues processed: 132 average time/residue: 0.0847 time to fit residues: 17.0538 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111650 restraints weight = 13469.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111132 restraints weight = 16955.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112129 restraints weight = 14140.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112178 restraints weight = 12307.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112357 restraints weight = 11000.522| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10176 Z= 0.121 Angle : 0.542 10.773 13848 Z= 0.273 Chirality : 0.038 0.152 1552 Planarity : 0.003 0.028 1738 Dihedral : 3.548 19.251 1340 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.05 % Allowed : 30.51 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.25), residues: 1230 helix: 2.76 (0.17), residues: 874 sheet: -2.17 (0.73), residues: 48 loop : -2.20 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.010 0.001 TYR B 26 PHE 0.014 0.001 PHE A 205 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00278 (10176) covalent geometry : angle 0.54235 (13848) hydrogen bonds : bond 0.04558 ( 682) hydrogen bonds : angle 3.26186 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.406 Fit side-chains REVERT: A 75 LEU cc_start: 0.8261 (mt) cc_final: 0.7662 (tp) REVERT: A 108 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: A 198 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 219 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7852 (tt) REVERT: A 309 CYS cc_start: 0.7046 (m) cc_final: 0.6509 (m) REVERT: A 495 LEU cc_start: 0.7818 (mp) cc_final: 0.7359 (mp) REVERT: A 521 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.7255 (t60) REVERT: B 75 LEU cc_start: 0.8284 (mt) cc_final: 0.7645 (tp) REVERT: B 108 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: B 122 MET cc_start: 0.8688 (ttm) cc_final: 0.8279 (ttm) REVERT: B 219 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 491 GLU cc_start: 0.6203 (tp30) cc_final: 0.5974 (tp30) REVERT: B 495 LEU cc_start: 0.7807 (mp) cc_final: 0.7502 (mp) REVERT: B 521 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7254 (t60) outliers start: 31 outliers final: 22 residues processed: 120 average time/residue: 0.0854 time to fit residues: 15.4348 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116933 restraints weight = 13474.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116426 restraints weight = 18505.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117100 restraints weight = 16426.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116565 restraints weight = 14812.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117002 restraints weight = 13457.415| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10176 Z= 0.111 Angle : 0.529 10.486 13848 Z= 0.265 Chirality : 0.037 0.147 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.444 18.887 1340 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.85 % Allowed : 30.51 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.25), residues: 1230 helix: 2.87 (0.17), residues: 874 sheet: -2.09 (0.75), residues: 48 loop : -2.16 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 45 TYR 0.009 0.001 TYR B 26 PHE 0.027 0.001 PHE A 205 TRP 0.012 0.001 TRP B 235 HIS 0.002 0.000 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00253 (10176) covalent geometry : angle 0.52921 (13848) hydrogen bonds : bond 0.04050 ( 682) hydrogen bonds : angle 3.16990 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.97 seconds wall clock time: 24 minutes 55.81 seconds (1495.81 seconds total)