Starting phenix.real_space_refine on Fri Nov 15 23:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_41454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_41454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_41454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_41454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tok_41454/11_2024/8tok_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.56, per 1000 atoms: 0.96 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 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: 1.00 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: 3.06 Time building geometry restraints manager: 3.13 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: 0.00 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: 1.390 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.180 Find NCS groups from input model: 0.280 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- 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 : 1.158 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2024 time to fit residues: 28.0883 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 : 1.156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 1.426 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.1843 time to fit residues: 33.1094 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 : 1.105 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1073 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= 0.178 Angle : 0.507 9.292 13848 Z= 0.259 Chirality : 0.037 0.150 1552 Planarity : 0.004 0.052 1738 Dihedral : 3.481 19.797 1340 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.85 % Allowed : 29.72 % Favored : 67.42 % 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: 2.29 (0.25), residues: 1230 helix: 2.87 (0.17), residues: 874 sheet: -1.42 (0.67), residues: 68 loop : -2.26 (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 A 611 PHE 0.012 0.001 PHE B 379 TYR 0.010 0.001 TYR B 26 ARG 0.001 0.000 ARG B 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 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.021 Fit side-chains REVERT: A 122 MET cc_start: 0.8604 (ttm) cc_final: 0.8194 (ttm) REVERT: A 175 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: A 509 MET cc_start: 0.8237 (mmp) cc_final: 0.7809 (mmp) REVERT: B 122 MET cc_start: 0.8635 (ttm) cc_final: 0.8202 (ttm) REVERT: B 175 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6799 (m-30) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.1920 time to fit residues: 33.9845 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1329 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= 0.199 Angle : 0.514 8.700 13848 Z= 0.262 Chirality : 0.038 0.148 1552 Planarity : 0.004 0.047 1738 Dihedral : 3.477 19.718 1340 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.54 % Allowed : 30.41 % 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: 2.23 (0.25), residues: 1230 helix: 2.82 (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 A 366 PHE 0.018 0.001 PHE B 379 TYR 0.010 0.001 TYR B 26 ARG 0.001 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.076 Fit side-chains REVERT: A 122 MET cc_start: 0.8605 (ttm) cc_final: 0.8226 (ttm) REVERT: A 219 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7745 (tt) REVERT: B 122 MET cc_start: 0.8621 (ttm) cc_final: 0.8214 (ttm) REVERT: B 219 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (tt) REVERT: B 491 GLU cc_start: 0.6078 (tp30) cc_final: 0.5871 (tp30) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 0.1868 time to fit residues: 34.7832 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 0.0060 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1523 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= 0.237 Angle : 0.556 8.326 13848 Z= 0.284 Chirality : 0.039 0.163 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.531 19.326 1340 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.94 % Allowed : 29.43 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.25), residues: 1230 helix: 2.75 (0.17), residues: 874 sheet: -1.58 (0.64), residues: 68 loop : -2.38 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 235 HIS 0.004 0.001 HIS B 611 PHE 0.016 0.001 PHE A 379 TYR 0.010 0.001 TYR B 26 ARG 0.002 0.000 ARG B 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 128 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 1.113 Fit side-chains REVERT: A 122 MET cc_start: 0.8617 (ttm) cc_final: 0.8217 (ttm) REVERT: A 219 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7885 (tt) REVERT: A 521 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.7250 (t60) REVERT: B 122 MET cc_start: 0.8657 (ttm) cc_final: 0.8252 (ttm) REVERT: B 219 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7893 (tt) REVERT: B 521 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7111 (t60) outliers start: 40 outliers final: 33 residues processed: 124 average time/residue: 0.1975 time to fit residues: 36.5244 Evaluate side-chains 120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 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 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 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10176 Z= 0.475 Angle : 0.691 8.722 13848 Z= 0.366 Chirality : 0.044 0.156 1552 Planarity : 0.004 0.034 1738 Dihedral : 4.060 19.458 1340 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.41 % Allowed : 28.35 % Favored : 66.24 % 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: 1.37 (0.24), residues: 1230 helix: 2.12 (0.17), residues: 874 sheet: -2.06 (0.70), residues: 48 loop : -2.30 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 695 HIS 0.006 0.001 HIS B 366 PHE 0.028 0.002 PHE A 379 TYR 0.015 0.002 TYR B 220 ARG 0.007 0.001 ARG A 45 *********************** 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 140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 85 time to evaluate : 1.152 Fit side-chains REVERT: A 219 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 521 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.7170 (t60) REVERT: B 219 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 521 TRP cc_start: 0.8292 (OUTLIER) cc_final: 0.7210 (t60) outliers start: 55 outliers final: 46 residues processed: 135 average time/residue: 0.1805 time to fit residues: 37.3379 Evaluate side-chains 130 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 48 THR 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 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 THR 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 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 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 381 THR 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 486 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1933 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= 0.206 Angle : 0.545 7.356 13848 Z= 0.281 Chirality : 0.038 0.144 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.794 19.396 1340 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.35 % Allowed : 31.10 % 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: 1.73 (0.24), residues: 1230 helix: 2.43 (0.17), residues: 874 sheet: -2.26 (0.71), residues: 48 loop : -2.28 (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 611 PHE 0.012 0.001 PHE A 379 TYR 0.012 0.001 TYR B 26 ARG 0.005 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 119 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.235 Fit side-chains REVERT: A 75 LEU cc_start: 0.8320 (mt) cc_final: 0.7859 (tt) REVERT: A 122 MET cc_start: 0.8622 (ttm) cc_final: 0.8264 (ttm) REVERT: A 219 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7886 (tt) REVERT: A 378 ASN cc_start: 0.8571 (m110) cc_final: 0.8362 (m110) REVERT: A 495 LEU cc_start: 0.8127 (mp) cc_final: 0.7810 (mp) REVERT: A 521 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.7095 (t60) REVERT: B 33 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7739 (mtm180) REVERT: B 219 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7878 (tt) REVERT: B 521 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.7171 (t60) outliers start: 34 outliers final: 22 residues processed: 115 average time/residue: 0.1945 time to fit residues: 33.8184 Evaluate side-chains 109 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 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 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 73 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1959 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= 0.223 Angle : 0.558 10.974 13848 Z= 0.282 Chirality : 0.038 0.143 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.697 19.213 1340 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.05 % Allowed : 31.10 % Favored : 65.85 % 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: 1.82 (0.25), residues: 1230 helix: 2.51 (0.17), residues: 874 sheet: -2.18 (0.72), residues: 48 loop : -2.30 (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 0.016 0.001 PHE A 205 TYR 0.011 0.001 TYR B 26 ARG 0.005 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 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.273 Fit side-chains REVERT: A 75 LEU cc_start: 0.8339 (mt) cc_final: 0.7922 (tt) REVERT: A 219 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 495 LEU cc_start: 0.8129 (mp) cc_final: 0.7778 (mp) REVERT: A 509 MET cc_start: 0.8336 (mmp) cc_final: 0.8034 (mmp) REVERT: A 521 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.7089 (t60) REVERT: B 75 LEU cc_start: 0.8323 (mt) cc_final: 0.7874 (tt) REVERT: B 219 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (tt) REVERT: B 509 MET cc_start: 0.8375 (mmp) cc_final: 0.8060 (mmp) REVERT: B 521 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7086 (t60) outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 0.1860 time to fit residues: 34.3800 Evaluate side-chains 108 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 616 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1924 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= 0.195 Angle : 0.544 10.895 13848 Z= 0.274 Chirality : 0.038 0.142 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.611 19.106 1340 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.56 % Allowed : 31.79 % Favored : 65.65 % 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: 1.95 (0.25), residues: 1230 helix: 2.61 (0.17), residues: 874 sheet: -2.25 (0.72), residues: 48 loop : -2.24 (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 0.015 0.001 PHE A 640 TYR 0.011 0.001 TYR B 26 ARG 0.005 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 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.150 Fit side-chains REVERT: A 75 LEU cc_start: 0.8330 (mt) cc_final: 0.7739 (tp) REVERT: A 219 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7738 (tt) REVERT: A 309 CYS cc_start: 0.7152 (m) cc_final: 0.6655 (m) REVERT: A 495 LEU cc_start: 0.8035 (mp) cc_final: 0.7652 (mp) REVERT: A 509 MET cc_start: 0.8319 (mmp) cc_final: 0.8038 (mmp) REVERT: A 521 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.7163 (t60) REVERT: B 75 LEU cc_start: 0.8351 (mt) cc_final: 0.7749 (tp) REVERT: B 219 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7734 (tt) REVERT: B 495 LEU cc_start: 0.8084 (mp) cc_final: 0.7826 (mt) REVERT: B 509 MET cc_start: 0.8322 (mmp) cc_final: 0.8039 (mmp) REVERT: B 521 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7173 (t60) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.1909 time to fit residues: 32.9999 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 : 1.049 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 616 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.2242 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2035 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= 0.261 Angle : 0.582 10.964 13848 Z= 0.296 Chirality : 0.039 0.168 1552 Planarity : 0.004 0.028 1738 Dihedral : 3.666 19.159 1340 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.95 % Allowed : 31.30 % Favored : 65.75 % 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: 1.86 (0.25), residues: 1230 helix: 2.52 (0.17), residues: 874 sheet: -2.10 (0.73), residues: 48 loop : -2.22 (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 611 PHE 0.019 0.001 PHE A 406 TYR 0.011 0.001 TYR A 26 ARG 0.005 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 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.064 Fit side-chains REVERT: A 75 LEU cc_start: 0.8324 (mt) cc_final: 0.7777 (tp) REVERT: A 219 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 495 LEU cc_start: 0.8133 (mp) cc_final: 0.7760 (mp) REVERT: A 509 MET cc_start: 0.8349 (mmp) cc_final: 0.8088 (mmp) REVERT: A 521 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.7219 (t60) REVERT: B 75 LEU cc_start: 0.8316 (mt) cc_final: 0.7890 (tt) REVERT: B 219 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 484 GLU cc_start: 0.8373 (pm20) cc_final: 0.7668 (mm-30) REVERT: B 509 MET cc_start: 0.8377 (mmp) cc_final: 0.8117 (mmp) REVERT: B 521 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.7226 (t60) outliers start: 30 outliers final: 25 residues processed: 113 average time/residue: 0.1870 time to fit residues: 32.1918 Evaluate side-chains 113 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 616 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 12 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111838 restraints weight = 13453.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111330 restraints weight = 17362.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113485 restraints weight = 15167.879| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1947 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= 0.181 Angle : 0.544 10.828 13848 Z= 0.273 Chirality : 0.037 0.142 1552 Planarity : 0.003 0.028 1738 Dihedral : 3.592 19.265 1340 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.85 % Allowed : 31.50 % Favored : 65.65 % 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: 2.68 (0.17), residues: 874 sheet: -2.21 (0.74), 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 0.013 0.001 PHE A 640 TYR 0.011 0.001 TYR A 26 ARG 0.004 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1785.72 seconds wall clock time: 33 minutes 27.12 seconds (2007.12 seconds total)