Starting phenix.real_space_refine on Wed Apr 30 19:50:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tok_41454/04_2025/8tok_41454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tok_41454/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tok_41454/04_2025/8tok_41454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tok_41454/04_2025/8tok_41454.map" model { file = "/net/cci-nas-00/data/ceres_data/8tok_41454/04_2025/8tok_41454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tok_41454/04_2025/8tok_41454.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 5, 'PHE:plan': 2, 'TYR:plan': 1} 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: 9.75, per 1000 atoms: 0.98 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.08 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: 3.07 Time building geometry restraints manager: 3.21 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.880 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (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 TRP 0.012 0.001 TRP A 521 HIS 0.003 0.000 HIS A 58 PHE 0.033 0.001 PHE B 315 TYR 0.006 0.001 TYR B 26 ARG 0.001 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.13969 ( 682) hydrogen bonds : angle 4.75697 ( 2016) covalent geometry : bond 0.00356 (10176) covalent geometry : angle 0.60191 (13848) *********************** 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 : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1965 time to fit residues: 26.8781 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 : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.143834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113538 restraints weight = 13393.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113310 restraints weight = 15737.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114596 restraints weight = 14052.730| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10176 Z= 0.135 Angle : 0.528 10.094 13848 Z= 0.272 Chirality : 0.038 0.155 1552 Planarity : 0.004 0.063 1738 Dihedral : 3.550 19.314 1340 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.56 % Allowed : 29.13 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1230 helix: 2.84 (0.17), residues: 862 sheet: -1.35 (0.68), residues: 68 loop : -2.26 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 533 HIS 0.003 0.001 HIS B 366 PHE 0.014 0.001 PHE A 315 TYR 0.009 0.001 TYR A 26 ARG 0.001 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 682) hydrogen bonds : angle 3.56140 ( 2016) covalent geometry : bond 0.00317 (10176) covalent geometry : angle 0.52786 (13848) *********************** 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 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.319 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.1965 time to fit residues: 35.2300 Evaluate side-chains 106 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 chunk 93 optimal weight: 0.0070 chunk 18 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 43 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.1362 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.150988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121576 restraints weight = 13365.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121104 restraints weight = 16745.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122193 restraints weight = 14674.840| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10176 Z= 0.100 Angle : 0.487 9.029 13848 Z= 0.247 Chirality : 0.036 0.150 1552 Planarity : 0.004 0.053 1738 Dihedral : 3.448 19.899 1340 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.87 % Allowed : 29.13 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.25), residues: 1230 helix: 3.01 (0.17), residues: 872 sheet: -1.48 (0.68), residues: 68 loop : -2.25 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 235 HIS 0.002 0.000 HIS B 366 PHE 0.010 0.001 PHE B 315 TYR 0.008 0.001 TYR A 188 ARG 0.001 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 682) hydrogen bonds : angle 3.25365 ( 2016) covalent geometry : bond 0.00217 (10176) covalent geometry : angle 0.48669 (13848) *********************** 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 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.058 Fit side-chains REVERT: A 48 THR cc_start: 0.7948 (m) cc_final: 0.7746 (m) REVERT: A 122 MET cc_start: 0.8614 (ttm) cc_final: 0.8388 (ttm) REVERT: A 509 MET cc_start: 0.8145 (mmp) cc_final: 0.7778 (mmp) REVERT: B 122 MET cc_start: 0.8616 (ttm) cc_final: 0.8334 (ttm) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.2160 time to fit residues: 37.4685 Evaluate side-chains 108 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 624 LEU 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 455 VAL Chi-restraints excluded: chain B residue 624 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116415 restraints weight = 13409.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115595 restraints weight = 20112.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116306 restraints weight = 17902.125| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1218 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= 0.128 Angle : 0.502 8.552 13848 Z= 0.257 Chirality : 0.038 0.150 1552 Planarity : 0.004 0.051 1738 Dihedral : 3.377 19.432 1340 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.76 % Allowed : 29.72 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.25), residues: 1230 helix: 2.92 (0.17), residues: 874 sheet: -1.44 (0.66), residues: 68 loop : -2.20 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 235 HIS 0.003 0.001 HIS B 611 PHE 0.020 0.001 PHE B 379 TYR 0.009 0.001 TYR B 26 ARG 0.001 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 682) hydrogen bonds : angle 3.22549 ( 2016) covalent geometry : bond 0.00303 (10176) covalent geometry : angle 0.50154 (13848) *********************** 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 120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.081 Fit side-chains REVERT: A 55 GLU cc_start: 0.7640 (mp0) cc_final: 0.7416 (mp0) REVERT: A 122 MET cc_start: 0.8656 (ttm) cc_final: 0.8313 (ttm) REVERT: A 491 GLU cc_start: 0.6186 (tp30) cc_final: 0.5979 (tp30) REVERT: B 122 MET cc_start: 0.8663 (ttm) cc_final: 0.8286 (ttm) REVERT: B 312 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7949 (tm) REVERT: B 491 GLU cc_start: 0.5981 (tp30) cc_final: 0.5758 (tp30) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 0.2011 time to fit residues: 35.0340 Evaluate side-chains 110 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 380 MET 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 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 312 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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 288 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.136942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106389 restraints weight = 13550.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105773 restraints weight = 18363.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106665 restraints weight = 15173.532| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10176 Z= 0.221 Angle : 0.617 8.753 13848 Z= 0.321 Chirality : 0.041 0.159 1552 Planarity : 0.004 0.045 1738 Dihedral : 3.690 19.663 1340 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.43 % Allowed : 28.35 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1230 helix: 2.52 (0.17), residues: 874 sheet: -1.54 (0.63), residues: 68 loop : -2.42 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.006 0.001 HIS B 611 PHE 0.020 0.002 PHE B 379 TYR 0.012 0.002 TYR B 220 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.06443 ( 682) hydrogen bonds : angle 3.62251 ( 2016) covalent geometry : bond 0.00544 (10176) covalent geometry : angle 0.61725 (13848) *********************** 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 136 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 1.162 Fit side-chains REVERT: A 219 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8095 (tt) REVERT: A 380 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: A 521 TRP cc_start: 0.8208 (OUTLIER) cc_final: 0.7274 (t60) REVERT: B 219 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 521 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7277 (t60) outliers start: 45 outliers final: 38 residues processed: 130 average time/residue: 0.1746 time to fit residues: 34.6445 Evaluate side-chains 126 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 134 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 240 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 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 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 20 VAL 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 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 240 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107183 restraints weight = 13762.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106438 restraints weight = 19736.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106796 restraints weight = 18731.784| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10176 Z= 0.218 Angle : 0.610 8.065 13848 Z= 0.318 Chirality : 0.041 0.145 1552 Planarity : 0.004 0.033 1738 Dihedral : 3.827 19.505 1340 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.12 % Allowed : 28.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1230 helix: 2.34 (0.17), residues: 874 sheet: -2.28 (0.69), residues: 48 loop : -2.27 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 695 HIS 0.005 0.001 HIS B 611 PHE 0.025 0.002 PHE A 205 TYR 0.013 0.002 TYR B 26 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.06345 ( 682) hydrogen bonds : angle 3.64304 ( 2016) covalent geometry : bond 0.00536 (10176) covalent geometry : angle 0.61011 (13848) *********************** 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 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 79 time to evaluate : 1.956 Fit side-chains REVERT: A 219 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8124 (tt) REVERT: A 380 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7463 (tpp) REVERT: A 521 TRP cc_start: 0.8266 (OUTLIER) cc_final: 0.7138 (t60) REVERT: B 219 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 521 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7150 (t60) REVERT: B 605 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (t) outliers start: 52 outliers final: 43 residues processed: 128 average time/residue: 0.1918 time to fit residues: 38.0094 Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 76 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 175 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL 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 380 MET Chi-restraints excluded: chain A residue 392 VAL 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 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 240 VAL Chi-restraints excluded: chain B residue 244 VAL 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 605 SER 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 42 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3515 r_free = 0.3515 target = 0.140708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110041 restraints weight = 13638.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109665 restraints weight = 17291.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111274 restraints weight = 14182.733| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1834 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= 0.130 Angle : 0.535 7.402 13848 Z= 0.272 Chirality : 0.038 0.142 1552 Planarity : 0.003 0.031 1738 Dihedral : 3.656 19.384 1340 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.44 % Allowed : 31.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1230 helix: 2.59 (0.17), residues: 874 sheet: -2.27 (0.71), residues: 48 loop : -2.26 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 235 HIS 0.003 0.001 HIS A 611 PHE 0.012 0.001 PHE A 205 TYR 0.011 0.001 TYR B 26 ARG 0.001 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 682) hydrogen bonds : angle 3.36390 ( 2016) covalent geometry : bond 0.00305 (10176) covalent geometry : angle 0.53470 (13848) *********************** 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 : 1.203 Fit side-chains REVERT: A 75 LEU cc_start: 0.8230 (mt) cc_final: 0.7742 (tt) REVERT: A 219 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 495 LEU cc_start: 0.7944 (mp) cc_final: 0.7677 (mt) REVERT: A 521 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7147 (t60) REVERT: B 219 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 521 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7126 (t60) outliers start: 35 outliers final: 26 residues processed: 123 average time/residue: 0.1928 time to fit residues: 36.2173 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain A residue 394 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 616 VAL 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 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 394 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 616 VAL 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 111 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.139265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108247 restraints weight = 13605.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107806 restraints weight = 16368.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108509 restraints weight = 13571.032| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1903 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= 0.152 Angle : 0.564 10.830 13848 Z= 0.285 Chirality : 0.039 0.143 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.636 19.355 1340 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.74 % Allowed : 29.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.25), residues: 1230 helix: 2.55 (0.17), residues: 874 sheet: -2.15 (0.72), residues: 48 loop : -2.24 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.004 0.001 HIS B 366 PHE 0.017 0.001 PHE A 205 TYR 0.011 0.001 TYR B 26 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.05241 ( 682) hydrogen bonds : angle 3.39184 ( 2016) covalent geometry : bond 0.00368 (10176) covalent geometry : angle 0.56421 (13848) *********************** 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 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 1.457 Fit side-chains REVERT: A 75 LEU cc_start: 0.8281 (mt) cc_final: 0.7833 (tt) REVERT: A 219 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7878 (tt) REVERT: A 378 ASN cc_start: 0.8407 (m110) cc_final: 0.8154 (m110) REVERT: A 521 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.7147 (t60) REVERT: A 605 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8318 (t) REVERT: B 75 LEU cc_start: 0.8265 (mt) cc_final: 0.7779 (tt) REVERT: B 219 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 484 GLU cc_start: 0.8386 (pm20) cc_final: 0.7630 (mm-30) REVERT: B 521 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.7148 (t60) outliers start: 38 outliers final: 28 residues processed: 121 average time/residue: 0.1850 time to fit residues: 34.0735 Evaluate side-chains 117 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 381 THR Chi-restraints excluded: chain A residue 394 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 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 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 394 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.138086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108139 restraints weight = 13677.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107744 restraints weight = 16880.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109064 restraints weight = 14363.866| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2001 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= 0.169 Angle : 0.579 10.686 13848 Z= 0.294 Chirality : 0.039 0.143 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.685 19.330 1340 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.54 % Allowed : 30.51 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1230 helix: 2.49 (0.17), residues: 874 sheet: -2.19 (0.72), residues: 48 loop : -2.26 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS B 366 PHE 0.015 0.001 PHE A 640 TYR 0.012 0.001 TYR B 26 ARG 0.003 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 682) hydrogen bonds : angle 3.45560 ( 2016) covalent geometry : bond 0.00410 (10176) covalent geometry : angle 0.57909 (13848) *********************** 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 120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.165 Fit side-chains REVERT: A 75 LEU cc_start: 0.8205 (mt) cc_final: 0.7628 (tp) REVERT: A 219 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 378 ASN cc_start: 0.8482 (m110) cc_final: 0.8212 (m110) REVERT: A 509 MET cc_start: 0.8473 (mmp) cc_final: 0.8145 (mmp) REVERT: A 521 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7107 (t60) REVERT: A 605 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 75 LEU cc_start: 0.8211 (mt) cc_final: 0.7760 (tt) REVERT: B 219 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 484 GLU cc_start: 0.8288 (pm20) cc_final: 0.7634 (mm-30) REVERT: B 521 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7095 (t60) outliers start: 36 outliers final: 30 residues processed: 120 average time/residue: 0.1820 time to fit residues: 33.1701 Evaluate side-chains 116 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 344 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 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 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 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 394 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3525 r_free = 0.3525 target = 0.141377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113459 restraints weight = 13702.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111925 restraints weight = 20186.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113549 restraints weight = 18985.140| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1891 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= 0.118 Angle : 0.541 10.600 13848 Z= 0.270 Chirality : 0.038 0.153 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.594 19.538 1340 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.85 % Allowed : 31.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1230 helix: 2.69 (0.17), residues: 874 sheet: -2.16 (0.74), residues: 48 loop : -2.21 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.003 0.001 HIS A 58 PHE 0.013 0.001 PHE A 205 TYR 0.010 0.001 TYR B 26 ARG 0.001 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 682) hydrogen bonds : angle 3.28372 ( 2016) covalent geometry : bond 0.00272 (10176) covalent geometry : angle 0.54059 (13848) ********************** 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 118 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 1.166 Fit side-chains REVERT: A 75 LEU cc_start: 0.8210 (mt) cc_final: 0.7608 (tp) REVERT: A 219 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 378 ASN cc_start: 0.8364 (m110) cc_final: 0.8073 (m110) REVERT: A 495 LEU cc_start: 0.7873 (mp) cc_final: 0.7486 (mp) REVERT: A 521 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7112 (t60) REVERT: B 75 LEU cc_start: 0.8211 (mt) cc_final: 0.7637 (tp) REVERT: B 219 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 484 GLU cc_start: 0.8183 (pm20) cc_final: 0.7553 (mm-30) REVERT: B 495 LEU cc_start: 0.7917 (mp) cc_final: 0.7604 (mt) REVERT: B 521 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7117 (t60) outliers start: 29 outliers final: 25 residues processed: 118 average time/residue: 0.1863 time to fit residues: 33.1806 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 : 1.108 ------------------------------------------------------------------------------- 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 381 THR 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 616 VAL 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 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 394 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 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3522 r_free = 0.3522 target = 0.140906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110381 restraints weight = 13579.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110023 restraints weight = 16227.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110887 restraints weight = 13597.041| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1919 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= 0.130 Angle : 0.549 10.901 13848 Z= 0.275 Chirality : 0.038 0.149 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.544 19.085 1340 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.35 % Allowed : 29.92 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1230 helix: 2.69 (0.17), residues: 874 sheet: -2.14 (0.73), residues: 48 loop : -2.15 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 235 HIS 0.003 0.001 HIS B 366 PHE 0.020 0.001 PHE A 406 TYR 0.010 0.001 TYR B 26 ARG 0.002 0.000 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 682) hydrogen bonds : angle 3.28832 ( 2016) covalent geometry : bond 0.00307 (10176) covalent geometry : angle 0.54922 (13848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2886.91 seconds wall clock time: 52 minutes 1.43 seconds (3121.43 seconds total)