Starting phenix.real_space_refine on Fri Feb 14 06:05:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tok_41454/02_2025/8tok_41454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tok_41454/02_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_41454/02_2025/8tok_41454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tok_41454/02_2025/8tok_41454.map" model { file = "/net/cci-nas-00/data/ceres_data/8tok_41454/02_2025/8tok_41454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tok_41454/02_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-5592/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: 9.44, per 1000 atoms: 0.95 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: 2.63 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: 0.90 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: 2.87 Time building geometry restraints manager: 3.00 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: 1.260 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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= 0.213 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 *********************** 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 : 0.984 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1973 time to fit residues: 26.7801 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 : 1.032 ------------------------------------------------------------------------------- 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 = 0.113309 restraints weight = 15739.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114058 restraints weight = 14054.781| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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= 0.201 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 *********************** 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 : 1.060 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.1874 time to fit residues: 32.9887 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 : 1.132 ------------------------------------------------------------------------------- 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: 0.9980 chunk 93 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117696 restraints weight = 13504.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115710 restraints weight = 12914.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115709 restraints weight = 11918.498| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1123 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= 0.186 Angle : 0.512 9.328 13848 Z= 0.262 Chirality : 0.037 0.149 1552 Planarity : 0.004 0.051 1738 Dihedral : 3.494 19.848 1340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.15 % Allowed : 29.82 % 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 (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: 2.26 (0.25), residues: 1230 helix: 2.85 (0.17), residues: 874 sheet: -1.44 (0.67), residues: 68 loop : -2.27 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 235 HIS 0.004 0.001 HIS A 611 PHE 0.013 0.001 PHE B 379 TYR 0.010 0.001 TYR B 26 ARG 0.001 0.000 ARG A 57 *********************** 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 : 1.159 Fit side-chains REVERT: A 122 MET cc_start: 0.8668 (ttm) cc_final: 0.8265 (ttm) REVERT: A 175 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6729 (m-30) REVERT: A 491 GLU cc_start: 0.6020 (tp30) cc_final: 0.5817 (tp30) REVERT: A 509 MET cc_start: 0.8130 (mmp) cc_final: 0.7768 (mmp) REVERT: B 122 MET cc_start: 0.8692 (ttm) cc_final: 0.8273 (ttm) REVERT: B 175 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6794 (m-30) outliers start: 32 outliers final: 23 residues processed: 121 average time/residue: 0.1978 time to fit residues: 35.4318 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 : 1.056 ------------------------------------------------------------------------------- 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 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 328 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 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 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 175 ASP 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 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3573 r_free = 0.3573 target = 0.145575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116975 restraints weight = 13284.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115535 restraints weight = 17212.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116465 restraints weight = 16814.269| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1241 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= 0.166 Angle : 0.506 8.477 13848 Z= 0.254 Chirality : 0.037 0.148 1552 Planarity : 0.003 0.046 1738 Dihedral : 3.455 19.801 1340 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.66 % Allowed : 31.30 % Favored : 66.04 % 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: 2.31 (0.25), residues: 1230 helix: 2.89 (0.17), residues: 874 sheet: -1.42 (0.65), residues: 68 loop : -2.30 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 PHE 0.014 0.001 PHE A 379 TYR 0.009 0.001 TYR B 26 ARG 0.002 0.000 ARG B 424 *********************** 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 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.113 Fit side-chains REVERT: A 122 MET cc_start: 0.8650 (ttm) cc_final: 0.8283 (ttm) REVERT: A 175 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: A 309 CYS cc_start: 0.7006 (m) cc_final: 0.6577 (m) REVERT: B 122 MET cc_start: 0.8654 (ttm) cc_final: 0.8258 (ttm) REVERT: B 175 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: B 491 GLU cc_start: 0.5994 (tp30) cc_final: 0.5772 (tp30) outliers start: 27 outliers final: 18 residues processed: 119 average time/residue: 0.1913 time to fit residues: 34.5686 Evaluate side-chains 112 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 455 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 124 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 455 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: 4.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101547 restraints weight = 13859.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101291 restraints weight = 17772.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101655 restraints weight = 16378.598| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 10176 Z= 0.597 Angle : 0.759 9.539 13848 Z= 0.405 Chirality : 0.047 0.163 1552 Planarity : 0.005 0.034 1738 Dihedral : 4.141 19.878 1340 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.51 % Allowed : 28.35 % 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: 1.16 (0.24), residues: 1230 helix: 1.96 (0.17), residues: 874 sheet: -1.44 (0.64), residues: 68 loop : -2.53 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 159 HIS 0.007 0.002 HIS B 366 PHE 0.030 0.003 PHE B 379 TYR 0.018 0.002 TYR B 279 ARG 0.004 0.001 ARG A 549 *********************** 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 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 88 time to evaluate : 1.150 Fit side-chains REVERT: A 217 SER cc_start: 0.8524 (t) cc_final: 0.7870 (p) REVERT: A 219 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 521 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7195 (t60) REVERT: A 529 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6830 (tt) REVERT: B 217 SER cc_start: 0.8523 (t) cc_final: 0.7846 (p) REVERT: B 219 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 521 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7197 (t60) REVERT: B 529 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6839 (tt) outliers start: 56 outliers final: 47 residues processed: 140 average time/residue: 0.1845 time to fit residues: 39.0490 Evaluate side-chains 133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 80 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 302 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 529 LEU 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 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 454 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 529 LEU 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: 0.8980 chunk 41 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.139965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109495 restraints weight = 13552.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109178 restraints weight = 17539.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110249 restraints weight = 14208.350| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1862 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= 0.199 Angle : 0.545 7.608 13848 Z= 0.282 Chirality : 0.039 0.146 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.809 19.551 1340 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.35 % Allowed : 31.99 % Favored : 64.67 % 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: 1.68 (0.24), residues: 1230 helix: 2.40 (0.17), residues: 874 sheet: -2.34 (0.69), residues: 48 loop : -2.28 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 PHE 0.013 0.001 PHE A 379 TYR 0.013 0.001 TYR B 26 ARG 0.001 0.000 ARG A 505 *********************** 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 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 1.120 Fit side-chains REVERT: A 122 MET cc_start: 0.8664 (ttm) cc_final: 0.8319 (ttm) REVERT: A 219 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7853 (tt) REVERT: A 495 LEU cc_start: 0.7981 (mp) cc_final: 0.7657 (mp) REVERT: A 509 MET cc_start: 0.8295 (mmp) cc_final: 0.7928 (mmp) REVERT: A 521 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7112 (t60) REVERT: B 122 MET cc_start: 0.8670 (ttm) cc_final: 0.8298 (ttm) REVERT: B 219 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 521 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7098 (t60) outliers start: 34 outliers final: 22 residues processed: 120 average time/residue: 0.1972 time to fit residues: 35.3086 Evaluate side-chains 111 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 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 175 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.139008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108352 restraints weight = 13752.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107730 restraints weight = 17200.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108484 restraints weight = 15639.624| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10176 Z= 0.228 Angle : 0.558 10.376 13848 Z= 0.284 Chirality : 0.039 0.142 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.701 19.260 1340 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.15 % Allowed : 31.79 % Favored : 65.06 % 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: 1.78 (0.25), residues: 1230 helix: 2.48 (0.17), residues: 874 sheet: -2.28 (0.70), residues: 48 loop : -2.29 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS B 611 PHE 0.012 0.001 PHE A 379 TYR 0.011 0.001 TYR B 26 ARG 0.007 0.000 ARG A 45 *********************** 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 118 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 1.085 Fit side-chains REVERT: A 75 LEU cc_start: 0.8237 (mt) cc_final: 0.7793 (tt) REVERT: A 219 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 521 TRP cc_start: 0.8203 (OUTLIER) cc_final: 0.7100 (t60) REVERT: A 605 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8316 (t) REVERT: B 219 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 521 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7098 (t60) REVERT: B 605 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8325 (t) outliers start: 32 outliers final: 26 residues processed: 117 average time/residue: 0.1797 time to fit residues: 31.7270 Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 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 175 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.138571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108056 restraints weight = 13656.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107495 restraints weight = 17976.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108576 restraints weight = 14491.876| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10176 Z= 0.240 Angle : 0.558 9.723 13848 Z= 0.285 Chirality : 0.039 0.143 1552 Planarity : 0.003 0.034 1738 Dihedral : 3.683 19.184 1340 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.35 % Allowed : 31.40 % Favored : 65.26 % 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: 1.79 (0.25), residues: 1230 helix: 2.49 (0.17), residues: 874 sheet: -2.22 (0.71), residues: 48 loop : -2.27 (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 0.016 0.001 PHE B 406 TYR 0.011 0.001 TYR B 26 ARG 0.006 0.000 ARG A 45 *********************** 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 119 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.158 Fit side-chains REVERT: A 75 LEU cc_start: 0.8266 (mt) cc_final: 0.7832 (tt) REVERT: A 219 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 521 TRP cc_start: 0.8203 (OUTLIER) cc_final: 0.7096 (t60) REVERT: A 605 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8362 (t) REVERT: B 75 LEU cc_start: 0.8250 (mt) cc_final: 0.7791 (tt) REVERT: B 219 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7858 (tt) REVERT: B 521 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7093 (t60) REVERT: B 605 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8346 (t) outliers start: 34 outliers final: 25 residues processed: 118 average time/residue: 0.1810 time to fit residues: 32.1479 Evaluate side-chains 113 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 175 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** B 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.141042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115547 restraints weight = 13598.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114249 restraints weight = 20619.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115089 restraints weight = 19214.916| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1910 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= 0.187 Angle : 0.536 9.975 13848 Z= 0.272 Chirality : 0.038 0.143 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.621 19.116 1340 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.25 % Allowed : 31.30 % Favored : 65.45 % 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: 1.96 (0.25), residues: 1230 helix: 2.63 (0.17), residues: 874 sheet: -2.26 (0.72), residues: 48 loop : -2.25 (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 366 PHE 0.012 0.001 PHE B 205 TYR 0.010 0.001 TYR B 26 ARG 0.006 0.000 ARG A 45 *********************** 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 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.934 Fit side-chains REVERT: A 75 LEU cc_start: 0.8241 (mt) cc_final: 0.7673 (tp) REVERT: A 108 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: A 219 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7691 (tt) REVERT: A 309 CYS cc_start: 0.7060 (m) cc_final: 0.6569 (m) REVERT: A 495 LEU cc_start: 0.7988 (mp) cc_final: 0.7570 (mp) REVERT: A 521 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7102 (t60) REVERT: B 75 LEU cc_start: 0.8232 (mt) cc_final: 0.7761 (tt) REVERT: B 219 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 495 LEU cc_start: 0.8019 (mp) cc_final: 0.7701 (mt) REVERT: B 509 MET cc_start: 0.8225 (mmp) cc_final: 0.7892 (mmp) REVERT: B 521 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7109 (t60) outliers start: 33 outliers final: 28 residues processed: 122 average time/residue: 0.1858 time to fit residues: 33.9270 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 : 0.870 ------------------------------------------------------------------------------- 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 101 ILE 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 175 ASP Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU 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 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 175 ASP Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 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 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: 0.9980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 114 optimal weight: 0.7980 chunk 40 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** 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 = 0.3543 r_free = 0.3543 target = 0.142766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112565 restraints weight = 13623.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112461 restraints weight = 15357.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113891 restraints weight = 13008.983| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1875 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= 0.169 Angle : 0.530 10.132 13848 Z= 0.267 Chirality : 0.037 0.149 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.534 19.301 1340 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.25 % Allowed : 31.40 % Favored : 65.35 % 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: 2.08 (0.25), residues: 1230 helix: 2.72 (0.17), residues: 874 sheet: -2.18 (0.74), residues: 48 loop : -2.22 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS B 58 PHE 0.020 0.001 PHE A 406 TYR 0.010 0.001 TYR A 26 ARG 0.006 0.000 ARG A 45 ********************** 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 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.003 Fit side-chains REVERT: A 75 LEU cc_start: 0.8217 (mt) cc_final: 0.7612 (tp) REVERT: A 108 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: A 309 CYS cc_start: 0.7011 (m) cc_final: 0.6458 (m) REVERT: A 491 GLU cc_start: 0.6253 (tp30) cc_final: 0.6031 (tp30) REVERT: A 495 LEU cc_start: 0.7728 (mp) cc_final: 0.7266 (mp) REVERT: A 521 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.7213 (t60) REVERT: B 75 LEU cc_start: 0.8231 (mt) cc_final: 0.7629 (tp) REVERT: B 108 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 309 CYS cc_start: 0.7003 (m) cc_final: 0.6476 (m) REVERT: B 484 GLU cc_start: 0.8336 (pm20) cc_final: 0.7607 (mm-30) REVERT: B 495 LEU cc_start: 0.7808 (mp) cc_final: 0.7541 (mt) REVERT: B 509 MET cc_start: 0.8252 (mmp) cc_final: 0.7898 (mmp) REVERT: B 521 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7224 (t60) outliers start: 33 outliers final: 24 residues processed: 121 average time/residue: 0.1803 time to fit residues: 32.7760 Evaluate side-chains 117 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 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 362 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 625 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.142626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116822 restraints weight = 13583.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115636 restraints weight = 17019.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116712 restraints weight = 16956.628| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1863 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= 0.176 Angle : 0.534 10.049 13848 Z= 0.267 Chirality : 0.037 0.143 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.488 19.463 1340 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.05 % Allowed : 31.59 % Favored : 65.35 % 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: 2.18 (0.25), residues: 1230 helix: 2.79 (0.17), residues: 874 sheet: -2.13 (0.75), residues: 48 loop : -2.17 (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 B 366 PHE 0.030 0.001 PHE A 205 TYR 0.009 0.001 TYR B 26 ARG 0.005 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.53 seconds wall clock time: 45 minutes 35.75 seconds (2735.75 seconds total)