Starting phenix.real_space_refine on Fri Mar 15 11:57:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyg_3861/03_2024/5oyg_3861.pdb" } resolution = 4.06 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= 0.004 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7566 2.51 5 N 1906 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 747": "NH1" <-> "NH2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 747": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11596 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5798 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 31, 'TRANS': 677} Chain breaks: 4 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5798 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 31, 'TRANS': 677} Chain breaks: 4 Time building chain proxies: 6.39, per 1000 atoms: 0.55 Number of scatterers: 11596 At special positions: 0 Unit cell: (85.995, 124.215, 121.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2052 8.00 N 1906 7.00 C 7566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.04 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 62.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.790A pdb=" N LEU A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.590A pdb=" N THR A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.596A pdb=" N THR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.704A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.643A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.638A pdb=" N THR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.767A pdb=" N ASN A 363 " --> pdb=" O VAL A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 408 through 438 Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.833A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.420A pdb=" N SER A 526 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 527 " --> pdb=" O MET A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 536 through 569 removed outlier: 3.538A pdb=" N ALA A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 removed outlier: 3.816A pdb=" N LEU A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 630 through 656 removed outlier: 3.952A pdb=" N LEU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 640 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 removed outlier: 4.062A pdb=" N ASN A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 715 removed outlier: 4.249A pdb=" N GLU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.586A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.009A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 removed outlier: 3.549A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 795 " --> pdb=" O TYR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 854 through 886 removed outlier: 4.038A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 909 removed outlier: 3.510A pdb=" N SER A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.791A pdb=" N LEU B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.597A pdb=" N THR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.703A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.644A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.638A pdb=" N THR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.766A pdb=" N ASN B 363 " --> pdb=" O VAL B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.833A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 519 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.421A pdb=" N SER B 526 " --> pdb=" O ALA B 523 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 527 " --> pdb=" O MET B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 536 through 569 removed outlier: 3.538A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 removed outlier: 3.815A pdb=" N LEU B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 630 through 656 removed outlier: 3.951A pdb=" N LEU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE B 640 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 641 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 654 " --> pdb=" O ASN B 650 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 removed outlier: 4.064A pdb=" N ASN B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 715 removed outlier: 4.254A pdb=" N GLU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 744 removed outlier: 3.587A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 781 removed outlier: 4.008A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 removed outlier: 3.549A pdb=" N LEU B 789 " --> pdb=" O PHE B 785 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 854 through 886 removed outlier: 4.036A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 886 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 909 removed outlier: 3.510A pdb=" N SER B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 4.024A pdb=" N SER A 196 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 123 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 126 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.658A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 812 through 813 Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 189 removed outlier: 4.022A pdb=" N SER B 196 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 123 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE B 126 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA7, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.659A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 812 through 813 616 hydrogen bonds defined for protein. 1830 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: 3.60 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3393 1.33 - 1.46: 2108 1.46 - 1.58: 6271 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11890 Sorted by residual: bond pdb=" CA ASP B 203 " pdb=" C ASP B 203 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.11e-02 8.12e+03 5.71e+00 bond pdb=" C MET A 176 " pdb=" N PRO A 177 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" CA ILE B 657 " pdb=" C ILE B 657 " ideal model delta sigma weight residual 1.524 1.549 -0.024 1.05e-02 9.07e+03 5.42e+00 bond pdb=" C MET B 176 " pdb=" N PRO B 177 " ideal model delta sigma weight residual 1.335 1.362 -0.028 1.19e-02 7.06e+03 5.42e+00 bond pdb=" CA ASP A 203 " pdb=" C ASP A 203 " ideal model delta sigma weight residual 1.521 1.547 -0.026 1.11e-02 8.12e+03 5.35e+00 ... (remaining 11885 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.03: 246 105.03 - 112.31: 5010 112.31 - 119.59: 4684 119.59 - 126.88: 6027 126.88 - 134.16: 127 Bond angle restraints: 16094 Sorted by residual: angle pdb=" C HIS B 453 " pdb=" N PRO B 454 " pdb=" CA PRO B 454 " ideal model delta sigma weight residual 119.87 114.38 5.49 1.04e+00 9.25e-01 2.79e+01 angle pdb=" C HIS A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta sigma weight residual 119.87 114.45 5.42 1.04e+00 9.25e-01 2.71e+01 angle pdb=" C ILE B 657 " pdb=" N PRO B 658 " pdb=" CA PRO B 658 " ideal model delta sigma weight residual 119.05 124.73 -5.68 1.11e+00 8.12e-01 2.62e+01 angle pdb=" C ILE A 657 " pdb=" N PRO A 658 " pdb=" CA PRO A 658 " ideal model delta sigma weight residual 119.05 124.68 -5.63 1.11e+00 8.12e-01 2.57e+01 angle pdb=" N SER A 811 " pdb=" CA SER A 811 " pdb=" C SER A 811 " ideal model delta sigma weight residual 110.91 116.32 -5.41 1.17e+00 7.31e-01 2.14e+01 ... (remaining 16089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 6441 16.26 - 32.52: 521 32.52 - 48.79: 122 48.79 - 65.05: 10 65.05 - 81.31: 12 Dihedral angle restraints: 7106 sinusoidal: 2910 harmonic: 4196 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -17.58 -68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -17.75 -68.25 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual 93.00 159.34 -66.34 1 1.00e+01 1.00e-02 5.75e+01 ... (remaining 7103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1249 0.100 - 0.200: 442 0.200 - 0.299: 59 0.299 - 0.399: 17 0.399 - 0.499: 7 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA PHE A 505 " pdb=" N PHE A 505 " pdb=" C PHE A 505 " pdb=" CB PHE A 505 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA PHE B 505 " pdb=" N PHE B 505 " pdb=" C PHE B 505 " pdb=" CB PHE B 505 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA THR A 594 " pdb=" N THR A 594 " pdb=" C THR A 594 " pdb=" CB THR A 594 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 1771 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 406 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.68e+00 pdb=" N PRO A 407 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO B 407 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 222 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO B 223 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " -0.036 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2743 2.81 - 3.33: 11084 3.33 - 3.85: 18028 3.85 - 4.38: 19669 4.38 - 4.90: 33725 Nonbonded interactions: 85249 Sorted by model distance: nonbonded pdb=" OH TYR B 791 " pdb=" O HIS B 802 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 791 " pdb=" O HIS A 802 " model vdw 2.283 2.440 nonbonded pdb=" NH2 ARG A 515 " pdb=" O MET A 622 " model vdw 2.334 2.520 nonbonded pdb=" NH2 ARG B 515 " pdb=" O MET B 622 " model vdw 2.334 2.520 nonbonded pdb=" O ALA A 600 " pdb=" OG1 THR A 782 " model vdw 2.336 2.440 ... (remaining 85244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.780 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: 4.240 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 31.460 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.007 0.037 11890 Z= 0.469 Angle : 1.269 9.151 16094 Z= 0.800 Chirality : 0.103 0.499 1774 Planarity : 0.007 0.074 2020 Dihedral : 12.530 81.310 4366 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.98 % Allowed : 6.58 % Favored : 91.44 % Cbeta Deviations : 0.74 % 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: -3.35 (0.19), residues: 1398 helix: -1.60 (0.15), residues: 790 sheet: -1.66 (0.98), residues: 22 loop : -3.11 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 334 HIS 0.006 0.002 HIS A 402 PHE 0.026 0.003 PHE B 585 TYR 0.023 0.003 TYR B 761 ARG 0.007 0.001 ARG B 618 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 268 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8397 (tmm) cc_final: 0.7400 (tmm) REVERT: A 222 TYR cc_start: 0.9286 (p90) cc_final: 0.8994 (p90) REVERT: A 342 LEU cc_start: 0.9863 (mt) cc_final: 0.9548 (tp) REVERT: A 364 ILE cc_start: 0.9699 (mp) cc_final: 0.9355 (mm) REVERT: A 391 MET cc_start: 0.9131 (tpt) cc_final: 0.8904 (tpp) REVERT: A 424 MET cc_start: 0.9274 (mmt) cc_final: 0.8993 (mmt) REVERT: A 429 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.9007 (mtm180) REVERT: A 461 ARG cc_start: 0.7096 (ttm170) cc_final: 0.6807 (tmt170) REVERT: A 551 ILE cc_start: 0.9748 (mt) cc_final: 0.9530 (mt) REVERT: A 553 LEU cc_start: 0.9873 (tp) cc_final: 0.8714 (tp) REVERT: A 557 TYR cc_start: 0.9245 (m-10) cc_final: 0.8433 (m-80) REVERT: A 588 LYS cc_start: 0.9262 (ttmp) cc_final: 0.9052 (tttp) REVERT: A 637 GLN cc_start: 0.9467 (tt0) cc_final: 0.9081 (tm-30) REVERT: A 688 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8898 (mt-10) REVERT: A 702 GLU cc_start: 0.8686 (tp30) cc_final: 0.7869 (tp30) REVERT: A 734 GLU cc_start: 0.9315 (tp30) cc_final: 0.8854 (tp30) REVERT: A 755 LYS cc_start: 0.9233 (ptmm) cc_final: 0.8699 (ptpt) REVERT: A 904 MET cc_start: 0.9407 (tmt) cc_final: 0.9114 (tmm) REVERT: B 117 MET cc_start: 0.8296 (tmm) cc_final: 0.7233 (tmm) REVERT: B 182 TYR cc_start: 0.9253 (m-80) cc_final: 0.9042 (m-80) REVERT: B 222 TYR cc_start: 0.9295 (p90) cc_final: 0.9006 (p90) REVERT: B 342 LEU cc_start: 0.9855 (mt) cc_final: 0.9492 (tp) REVERT: B 391 MET cc_start: 0.9168 (tpt) cc_final: 0.8947 (tpp) REVERT: B 424 MET cc_start: 0.9281 (mmt) cc_final: 0.9018 (mmt) REVERT: B 429 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (mtm180) REVERT: B 461 ARG cc_start: 0.6959 (ttm170) cc_final: 0.6664 (tmt170) REVERT: B 553 LEU cc_start: 0.9864 (tp) cc_final: 0.8702 (tp) REVERT: B 557 TYR cc_start: 0.9178 (m-10) cc_final: 0.8347 (m-80) REVERT: B 688 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8887 (mt-10) REVERT: B 702 GLU cc_start: 0.8678 (tp30) cc_final: 0.7875 (tp30) REVERT: B 734 GLU cc_start: 0.9310 (tp30) cc_final: 0.8863 (tp30) REVERT: B 745 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8646 (mt-10) REVERT: B 755 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8740 (ptpt) REVERT: B 904 MET cc_start: 0.9402 (tmt) cc_final: 0.9078 (tmm) outliers start: 25 outliers final: 0 residues processed: 285 average time/residue: 0.2930 time to fit residues: 111.0554 Evaluate side-chains 175 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 646 GLN ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11890 Z= 0.232 Angle : 0.675 10.722 16094 Z= 0.349 Chirality : 0.043 0.184 1774 Planarity : 0.005 0.057 2020 Dihedral : 5.193 22.739 1562 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % 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: -1.13 (0.22), residues: 1398 helix: 0.53 (0.17), residues: 838 sheet: -1.24 (0.91), residues: 28 loop : -2.91 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 427 HIS 0.005 0.001 HIS B 402 PHE 0.040 0.001 PHE B 505 TYR 0.013 0.001 TYR B 119 ARG 0.005 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8303 (tmm) cc_final: 0.7155 (tmm) REVERT: A 222 TYR cc_start: 0.9255 (p90) cc_final: 0.8999 (p90) REVERT: A 252 GLU cc_start: 0.9511 (tp30) cc_final: 0.9106 (tp30) REVERT: A 368 GLU cc_start: 0.9213 (mp0) cc_final: 0.8846 (mp0) REVERT: A 378 MET cc_start: 0.8650 (mpp) cc_final: 0.8428 (mpp) REVERT: A 461 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6784 (tmt170) REVERT: A 545 ILE cc_start: 0.9650 (tp) cc_final: 0.9441 (pt) REVERT: A 702 GLU cc_start: 0.9085 (tp30) cc_final: 0.8277 (tp30) REVERT: A 734 GLU cc_start: 0.9347 (tp30) cc_final: 0.8857 (tp30) REVERT: A 755 LYS cc_start: 0.9305 (ptmm) cc_final: 0.8875 (ptpp) REVERT: A 840 ASP cc_start: 0.9234 (t0) cc_final: 0.8969 (t70) REVERT: A 881 PHE cc_start: 0.9168 (t80) cc_final: 0.8727 (t80) REVERT: A 904 MET cc_start: 0.9524 (tmm) cc_final: 0.9314 (tmm) REVERT: A 909 MET cc_start: 0.7802 (ppp) cc_final: 0.7556 (ppp) REVERT: B 117 MET cc_start: 0.8311 (tmm) cc_final: 0.7127 (tmm) REVERT: B 206 GLN cc_start: 0.9469 (tt0) cc_final: 0.9256 (tt0) REVERT: B 222 TYR cc_start: 0.9248 (p90) cc_final: 0.9042 (p90) REVERT: B 252 GLU cc_start: 0.9571 (tp30) cc_final: 0.9262 (tp30) REVERT: B 342 LEU cc_start: 0.9882 (mt) cc_final: 0.9659 (tp) REVERT: B 367 MET cc_start: 0.9324 (mtt) cc_final: 0.9094 (mtt) REVERT: B 368 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9125 (mm-30) REVERT: B 369 MET cc_start: 0.9054 (mtm) cc_final: 0.8703 (ttm) REVERT: B 378 MET cc_start: 0.8602 (mpp) cc_final: 0.8388 (mpp) REVERT: B 461 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6747 (tmt170) REVERT: B 688 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8874 (mt-10) REVERT: B 702 GLU cc_start: 0.9135 (tp30) cc_final: 0.8221 (tp30) REVERT: B 704 MET cc_start: 0.9305 (tpp) cc_final: 0.8943 (tpp) REVERT: B 734 GLU cc_start: 0.9328 (tp30) cc_final: 0.8864 (tp30) REVERT: B 755 LYS cc_start: 0.9321 (ptmm) cc_final: 0.8840 (ptpp) REVERT: B 794 MET cc_start: 0.8648 (mmp) cc_final: 0.8357 (mmp) REVERT: B 831 TYR cc_start: 0.6449 (m-10) cc_final: 0.6183 (m-80) REVERT: B 840 ASP cc_start: 0.9189 (t0) cc_final: 0.8902 (t70) REVERT: B 881 PHE cc_start: 0.9195 (t80) cc_final: 0.8821 (t80) REVERT: B 904 MET cc_start: 0.9526 (tmm) cc_final: 0.9259 (tmm) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.2502 time to fit residues: 72.4964 Evaluate side-chains 147 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.0070 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 206 GLN A 818 GLN B 183 HIS ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11890 Z= 0.279 Angle : 0.670 9.843 16094 Z= 0.349 Chirality : 0.044 0.184 1774 Planarity : 0.005 0.059 2020 Dihedral : 5.012 22.049 1562 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % 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: -0.46 (0.23), residues: 1398 helix: 1.25 (0.17), residues: 842 sheet: -2.16 (0.80), residues: 44 loop : -2.94 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 427 HIS 0.006 0.001 HIS A 402 PHE 0.038 0.002 PHE A 505 TYR 0.014 0.002 TYR B 119 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8115 (tmm) cc_final: 0.7006 (tmm) REVERT: A 222 TYR cc_start: 0.9245 (p90) cc_final: 0.9001 (p90) REVERT: A 252 GLU cc_start: 0.9506 (tp30) cc_final: 0.9165 (tp30) REVERT: A 341 MET cc_start: 0.9253 (tpp) cc_final: 0.8896 (tpp) REVERT: A 367 MET cc_start: 0.9165 (mtt) cc_final: 0.8943 (mtt) REVERT: A 368 GLU cc_start: 0.9229 (mp0) cc_final: 0.8595 (mp0) REVERT: A 369 MET cc_start: 0.9175 (mtt) cc_final: 0.8715 (ttm) REVERT: A 378 MET cc_start: 0.8768 (mpp) cc_final: 0.8494 (mpp) REVERT: A 461 ARG cc_start: 0.7079 (ttm170) cc_final: 0.6783 (tmt170) REVERT: A 702 GLU cc_start: 0.8853 (tp30) cc_final: 0.7784 (tp30) REVERT: A 705 GLU cc_start: 0.8980 (pm20) cc_final: 0.8769 (pm20) REVERT: A 734 GLU cc_start: 0.9231 (tp30) cc_final: 0.8609 (tp30) REVERT: A 755 LYS cc_start: 0.9347 (ptmm) cc_final: 0.8982 (ptpp) REVERT: A 840 ASP cc_start: 0.9249 (t0) cc_final: 0.8891 (t70) REVERT: A 881 PHE cc_start: 0.9146 (t80) cc_final: 0.8727 (t80) REVERT: A 909 MET cc_start: 0.7629 (ppp) cc_final: 0.7333 (ppp) REVERT: B 117 MET cc_start: 0.8156 (tmm) cc_final: 0.7022 (tmm) REVERT: B 206 GLN cc_start: 0.9435 (tt0) cc_final: 0.9170 (tt0) REVERT: B 222 TYR cc_start: 0.9264 (p90) cc_final: 0.9012 (p90) REVERT: B 252 GLU cc_start: 0.9574 (tp30) cc_final: 0.9324 (tp30) REVERT: B 342 LEU cc_start: 0.9919 (mt) cc_final: 0.9698 (tp) REVERT: B 368 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9087 (mm-30) REVERT: B 369 MET cc_start: 0.9131 (mtm) cc_final: 0.8648 (ttm) REVERT: B 378 MET cc_start: 0.8596 (mpp) cc_final: 0.8217 (mpp) REVERT: B 461 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6758 (tmt170) REVERT: B 702 GLU cc_start: 0.8856 (tp30) cc_final: 0.8369 (tp30) REVERT: B 734 GLU cc_start: 0.9229 (tp30) cc_final: 0.8546 (tp30) REVERT: B 755 LYS cc_start: 0.9362 (ptmm) cc_final: 0.8842 (ptpp) REVERT: B 794 MET cc_start: 0.8691 (mmp) cc_final: 0.8347 (mmp) REVERT: B 831 TYR cc_start: 0.6816 (m-10) cc_final: 0.6572 (m-80) REVERT: B 840 ASP cc_start: 0.9211 (t0) cc_final: 0.8880 (t70) REVERT: B 881 PHE cc_start: 0.9157 (t80) cc_final: 0.8764 (t80) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2500 time to fit residues: 61.2147 Evaluate side-chains 136 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11890 Z= 0.177 Angle : 0.615 9.364 16094 Z= 0.314 Chirality : 0.042 0.209 1774 Planarity : 0.004 0.054 2020 Dihedral : 4.761 21.104 1562 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % 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: -0.11 (0.23), residues: 1398 helix: 1.56 (0.18), residues: 844 sheet: -1.87 (0.77), residues: 48 loop : -2.87 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 427 HIS 0.002 0.000 HIS B 402 PHE 0.014 0.001 PHE B 505 TYR 0.016 0.001 TYR A 687 ARG 0.002 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8292 (tmm) cc_final: 0.7249 (tmm) REVERT: A 252 GLU cc_start: 0.9442 (tp30) cc_final: 0.9092 (tp30) REVERT: A 341 MET cc_start: 0.9279 (tpp) cc_final: 0.8925 (tpp) REVERT: A 367 MET cc_start: 0.9095 (mtt) cc_final: 0.8447 (mtt) REVERT: A 368 GLU cc_start: 0.9252 (mp0) cc_final: 0.8723 (mp0) REVERT: A 378 MET cc_start: 0.8686 (mpp) cc_final: 0.8440 (mpp) REVERT: A 461 ARG cc_start: 0.7186 (ttm170) cc_final: 0.6895 (tmt170) REVERT: A 702 GLU cc_start: 0.8683 (tp30) cc_final: 0.7308 (tp30) REVERT: A 734 GLU cc_start: 0.9156 (tp30) cc_final: 0.8719 (tp30) REVERT: A 755 LYS cc_start: 0.9342 (ptmm) cc_final: 0.8636 (mttm) REVERT: A 840 ASP cc_start: 0.9090 (t0) cc_final: 0.8716 (t70) REVERT: A 881 PHE cc_start: 0.9070 (t80) cc_final: 0.8727 (t80) REVERT: B 117 MET cc_start: 0.8374 (tmm) cc_final: 0.7285 (tmm) REVERT: B 126 PHE cc_start: 0.8935 (t80) cc_final: 0.8724 (t80) REVERT: B 222 TYR cc_start: 0.9259 (p90) cc_final: 0.9034 (p90) REVERT: B 252 GLU cc_start: 0.9555 (tp30) cc_final: 0.9248 (tp30) REVERT: B 367 MET cc_start: 0.9391 (mtm) cc_final: 0.8952 (mtt) REVERT: B 368 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9085 (mm-30) REVERT: B 378 MET cc_start: 0.8691 (mpp) cc_final: 0.8480 (mpp) REVERT: B 461 ARG cc_start: 0.7059 (ttm170) cc_final: 0.6773 (tmt170) REVERT: B 702 GLU cc_start: 0.8600 (tp30) cc_final: 0.7843 (tp30) REVERT: B 705 GLU cc_start: 0.9096 (pm20) cc_final: 0.8887 (pm20) REVERT: B 734 GLU cc_start: 0.9168 (tp30) cc_final: 0.8591 (tp30) REVERT: B 755 LYS cc_start: 0.9303 (ptmm) cc_final: 0.8855 (ptpp) REVERT: B 794 MET cc_start: 0.8818 (mmp) cc_final: 0.8458 (mmp) REVERT: B 840 ASP cc_start: 0.9069 (t0) cc_final: 0.8682 (t70) REVERT: B 881 PHE cc_start: 0.9074 (t80) cc_final: 0.8720 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2484 time to fit residues: 65.2337 Evaluate side-chains 141 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 0.0000 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11890 Z= 0.156 Angle : 0.604 9.025 16094 Z= 0.305 Chirality : 0.041 0.174 1774 Planarity : 0.004 0.049 2020 Dihedral : 4.563 20.589 1562 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.08 % Allowed : 2.30 % Favored : 97.62 % 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: 0.15 (0.24), residues: 1398 helix: 1.75 (0.18), residues: 846 sheet: -1.67 (0.79), residues: 48 loop : -2.79 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 427 HIS 0.002 0.000 HIS B 230 PHE 0.020 0.001 PHE A 505 TYR 0.016 0.001 TYR B 687 ARG 0.005 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8389 (tmm) cc_final: 0.7350 (tmm) REVERT: A 222 TYR cc_start: 0.9341 (p90) cc_final: 0.9059 (p90) REVERT: A 252 GLU cc_start: 0.9413 (tp30) cc_final: 0.9051 (tp30) REVERT: A 341 MET cc_start: 0.9280 (tpp) cc_final: 0.8860 (tpp) REVERT: A 367 MET cc_start: 0.9089 (mtt) cc_final: 0.8331 (mtt) REVERT: A 368 GLU cc_start: 0.9248 (mp0) cc_final: 0.8786 (mp0) REVERT: A 378 MET cc_start: 0.8731 (mpp) cc_final: 0.8523 (mpp) REVERT: A 461 ARG cc_start: 0.7289 (ttm170) cc_final: 0.7009 (tmt170) REVERT: A 702 GLU cc_start: 0.8384 (tp30) cc_final: 0.7331 (tp30) REVERT: A 704 MET cc_start: 0.9238 (tpp) cc_final: 0.9019 (tpp) REVERT: A 734 GLU cc_start: 0.9141 (tp30) cc_final: 0.8794 (tp30) REVERT: A 755 LYS cc_start: 0.9353 (ptmm) cc_final: 0.8844 (mtmm) REVERT: A 840 ASP cc_start: 0.9067 (t0) cc_final: 0.8693 (t70) REVERT: A 881 PHE cc_start: 0.9046 (t80) cc_final: 0.8703 (t80) REVERT: B 117 MET cc_start: 0.8395 (tmm) cc_final: 0.7688 (tmm) REVERT: B 222 TYR cc_start: 0.9260 (p90) cc_final: 0.8957 (p90) REVERT: B 252 GLU cc_start: 0.9545 (tp30) cc_final: 0.9241 (tp30) REVERT: B 342 LEU cc_start: 0.9895 (mt) cc_final: 0.9660 (tp) REVERT: B 367 MET cc_start: 0.9432 (mtm) cc_final: 0.8982 (mtt) REVERT: B 368 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9034 (mm-30) REVERT: B 378 MET cc_start: 0.8730 (mpp) cc_final: 0.8443 (mpp) REVERT: B 461 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6773 (tmt170) REVERT: B 557 TYR cc_start: 0.8848 (m-10) cc_final: 0.8269 (m-80) REVERT: B 702 GLU cc_start: 0.8422 (tp30) cc_final: 0.7799 (tp30) REVERT: B 705 GLU cc_start: 0.8991 (pm20) cc_final: 0.8758 (pm20) REVERT: B 734 GLU cc_start: 0.9124 (tp30) cc_final: 0.8397 (tp30) REVERT: B 738 ASP cc_start: 0.8286 (m-30) cc_final: 0.6965 (m-30) REVERT: B 755 LYS cc_start: 0.9356 (ptmm) cc_final: 0.8825 (ptpp) REVERT: B 794 MET cc_start: 0.8727 (mmp) cc_final: 0.8407 (mmp) REVERT: B 840 ASP cc_start: 0.9126 (t0) cc_final: 0.8736 (t70) REVERT: B 881 PHE cc_start: 0.9052 (t80) cc_final: 0.8708 (t80) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2404 time to fit residues: 67.9760 Evaluate side-chains 150 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11890 Z= 0.316 Angle : 0.683 9.971 16094 Z= 0.357 Chirality : 0.044 0.174 1774 Planarity : 0.004 0.047 2020 Dihedral : 4.757 21.411 1562 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1398 helix: 1.83 (0.18), residues: 840 sheet: -1.78 (0.77), residues: 48 loop : -2.84 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.006 0.001 HIS B 402 PHE 0.025 0.002 PHE A 505 TYR 0.017 0.002 TYR A 687 ARG 0.007 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8295 (tmm) cc_final: 0.8058 (tmm) REVERT: A 222 TYR cc_start: 0.9293 (p90) cc_final: 0.9004 (p90) REVERT: A 252 GLU cc_start: 0.9541 (tp30) cc_final: 0.9237 (tp30) REVERT: A 341 MET cc_start: 0.9420 (tpp) cc_final: 0.9048 (tpp) REVERT: A 367 MET cc_start: 0.9204 (mtt) cc_final: 0.8577 (mtt) REVERT: A 368 GLU cc_start: 0.9271 (mp0) cc_final: 0.8688 (mp0) REVERT: A 369 MET cc_start: 0.9047 (mmm) cc_final: 0.8671 (mpp) REVERT: A 378 MET cc_start: 0.8753 (mpp) cc_final: 0.8476 (mpp) REVERT: A 424 MET cc_start: 0.8818 (mmm) cc_final: 0.8540 (mmm) REVERT: A 461 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6878 (tmt170) REVERT: A 690 ASP cc_start: 0.9547 (m-30) cc_final: 0.9337 (m-30) REVERT: A 702 GLU cc_start: 0.8607 (tp30) cc_final: 0.7810 (tp30) REVERT: A 734 GLU cc_start: 0.9280 (tp30) cc_final: 0.8673 (tp30) REVERT: A 755 LYS cc_start: 0.9302 (ptmm) cc_final: 0.9002 (ptpp) REVERT: A 840 ASP cc_start: 0.9258 (t0) cc_final: 0.8812 (t70) REVERT: A 881 PHE cc_start: 0.9078 (t80) cc_final: 0.8734 (t80) REVERT: B 117 MET cc_start: 0.8291 (tmm) cc_final: 0.8050 (tmm) REVERT: B 206 GLN cc_start: 0.8815 (mt0) cc_final: 0.8613 (mt0) REVERT: B 222 TYR cc_start: 0.9253 (p90) cc_final: 0.8922 (p90) REVERT: B 252 GLU cc_start: 0.9582 (tp30) cc_final: 0.9325 (tp30) REVERT: B 367 MET cc_start: 0.9399 (mtm) cc_final: 0.8960 (mtt) REVERT: B 368 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9106 (mm-30) REVERT: B 369 MET cc_start: 0.9015 (mtp) cc_final: 0.8536 (ttm) REVERT: B 378 MET cc_start: 0.8710 (mpp) cc_final: 0.8383 (mpp) REVERT: B 461 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6894 (tmt170) REVERT: B 702 GLU cc_start: 0.8621 (tp30) cc_final: 0.7820 (tp30) REVERT: B 705 GLU cc_start: 0.9070 (pm20) cc_final: 0.8754 (pm20) REVERT: B 734 GLU cc_start: 0.9279 (tp30) cc_final: 0.8675 (tp30) REVERT: B 755 LYS cc_start: 0.9296 (ptmm) cc_final: 0.8688 (ptpp) REVERT: B 794 MET cc_start: 0.8627 (mmp) cc_final: 0.8393 (mmp) REVERT: B 840 ASP cc_start: 0.9251 (t0) cc_final: 0.8805 (t70) REVERT: B 881 PHE cc_start: 0.9088 (t80) cc_final: 0.8744 (t80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2196 time to fit residues: 55.2356 Evaluate side-chains 132 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11890 Z= 0.184 Angle : 0.635 8.746 16094 Z= 0.317 Chirality : 0.042 0.171 1774 Planarity : 0.004 0.047 2020 Dihedral : 4.576 20.377 1562 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 0.42 (0.24), residues: 1398 helix: 2.02 (0.18), residues: 844 sheet: -1.68 (0.80), residues: 48 loop : -2.74 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.003 0.001 HIS A 402 PHE 0.029 0.001 PHE A 505 TYR 0.024 0.001 TYR A 687 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.9021 (t80) cc_final: 0.8787 (t80) REVERT: A 222 TYR cc_start: 0.9288 (p90) cc_final: 0.8999 (p90) REVERT: A 252 GLU cc_start: 0.9511 (tp30) cc_final: 0.9218 (tp30) REVERT: A 341 MET cc_start: 0.9394 (tpp) cc_final: 0.9024 (tpp) REVERT: A 367 MET cc_start: 0.9203 (mtt) cc_final: 0.8563 (mtt) REVERT: A 368 GLU cc_start: 0.9198 (mp0) cc_final: 0.8582 (mp0) REVERT: A 369 MET cc_start: 0.8986 (mmm) cc_final: 0.8650 (mpp) REVERT: A 378 MET cc_start: 0.8774 (mpp) cc_final: 0.8516 (mpp) REVERT: A 461 ARG cc_start: 0.7168 (ttm170) cc_final: 0.6872 (tmt170) REVERT: A 702 GLU cc_start: 0.8396 (tp30) cc_final: 0.7942 (tp30) REVERT: A 734 GLU cc_start: 0.9190 (tp30) cc_final: 0.8417 (tp30) REVERT: A 738 ASP cc_start: 0.8388 (m-30) cc_final: 0.7001 (m-30) REVERT: A 755 LYS cc_start: 0.9395 (ptmm) cc_final: 0.8803 (ptpp) REVERT: A 840 ASP cc_start: 0.9091 (t0) cc_final: 0.8662 (t70) REVERT: A 881 PHE cc_start: 0.9067 (t80) cc_final: 0.8703 (t80) REVERT: B 117 MET cc_start: 0.8441 (tmm) cc_final: 0.8220 (tmm) REVERT: B 126 PHE cc_start: 0.9008 (t80) cc_final: 0.8779 (t80) REVERT: B 222 TYR cc_start: 0.9243 (p90) cc_final: 0.8899 (p90) REVERT: B 252 GLU cc_start: 0.9568 (tp30) cc_final: 0.9288 (tp30) REVERT: B 367 MET cc_start: 0.9358 (mtm) cc_final: 0.8890 (mtt) REVERT: B 368 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9150 (mm-30) REVERT: B 369 MET cc_start: 0.9066 (mtp) cc_final: 0.8543 (ttm) REVERT: B 378 MET cc_start: 0.8850 (mpp) cc_final: 0.8591 (mpp) REVERT: B 461 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6835 (tmt170) REVERT: B 702 GLU cc_start: 0.8426 (tp30) cc_final: 0.7965 (tp30) REVERT: B 734 GLU cc_start: 0.9205 (tp30) cc_final: 0.8444 (tp30) REVERT: B 738 ASP cc_start: 0.8362 (m-30) cc_final: 0.6976 (m-30) REVERT: B 755 LYS cc_start: 0.9206 (ptmm) cc_final: 0.8701 (ptpp) REVERT: B 794 MET cc_start: 0.8582 (mmp) cc_final: 0.8331 (mmp) REVERT: B 840 ASP cc_start: 0.9083 (t0) cc_final: 0.8655 (t70) REVERT: B 881 PHE cc_start: 0.9072 (t80) cc_final: 0.8709 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2411 time to fit residues: 60.5361 Evaluate side-chains 136 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.0470 chunk 91 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11890 Z= 0.160 Angle : 0.631 8.740 16094 Z= 0.316 Chirality : 0.042 0.208 1774 Planarity : 0.004 0.047 2020 Dihedral : 4.529 20.274 1562 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.48 (0.24), residues: 1398 helix: 2.05 (0.18), residues: 838 sheet: -1.58 (0.82), residues: 48 loop : -2.63 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.002 0.001 HIS B 402 PHE 0.018 0.001 PHE A 712 TYR 0.024 0.001 TYR A 687 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8381 (tmm) cc_final: 0.7916 (tmm) REVERT: A 126 PHE cc_start: 0.8959 (t80) cc_final: 0.8729 (t80) REVERT: A 222 TYR cc_start: 0.9313 (p90) cc_final: 0.9002 (p90) REVERT: A 252 GLU cc_start: 0.9505 (tp30) cc_final: 0.9158 (tp30) REVERT: A 341 MET cc_start: 0.9296 (tpp) cc_final: 0.8895 (tpp) REVERT: A 367 MET cc_start: 0.9035 (mtt) cc_final: 0.8463 (mtt) REVERT: A 368 GLU cc_start: 0.9195 (mp0) cc_final: 0.8760 (mp0) REVERT: A 369 MET cc_start: 0.8898 (mmm) cc_final: 0.8575 (mpp) REVERT: A 461 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6966 (tmt170) REVERT: A 702 GLU cc_start: 0.8322 (tp30) cc_final: 0.7218 (tp30) REVERT: A 734 GLU cc_start: 0.9169 (tp30) cc_final: 0.8561 (tp30) REVERT: A 738 ASP cc_start: 0.8332 (m-30) cc_final: 0.7546 (m-30) REVERT: A 755 LYS cc_start: 0.9378 (ptmm) cc_final: 0.8830 (ptpp) REVERT: A 840 ASP cc_start: 0.9077 (t0) cc_final: 0.8654 (t70) REVERT: A 881 PHE cc_start: 0.9052 (t80) cc_final: 0.8651 (t80) REVERT: B 126 PHE cc_start: 0.8978 (t80) cc_final: 0.8754 (t80) REVERT: B 222 TYR cc_start: 0.9240 (p90) cc_final: 0.8883 (p90) REVERT: B 252 GLU cc_start: 0.9565 (tp30) cc_final: 0.9279 (tp30) REVERT: B 342 LEU cc_start: 0.9929 (mt) cc_final: 0.9645 (tp) REVERT: B 367 MET cc_start: 0.9390 (mtm) cc_final: 0.8954 (mtt) REVERT: B 368 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9145 (mm-30) REVERT: B 369 MET cc_start: 0.8928 (mtp) cc_final: 0.8425 (ttm) REVERT: B 461 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6945 (tmt170) REVERT: B 499 PHE cc_start: 0.9042 (t80) cc_final: 0.8813 (t80) REVERT: B 702 GLU cc_start: 0.8355 (tp30) cc_final: 0.7455 (tp30) REVERT: B 734 GLU cc_start: 0.9186 (tp30) cc_final: 0.8548 (tp30) REVERT: B 738 ASP cc_start: 0.8322 (m-30) cc_final: 0.7551 (m-30) REVERT: B 755 LYS cc_start: 0.9220 (ptmm) cc_final: 0.8816 (ptpp) REVERT: B 794 MET cc_start: 0.8566 (mmp) cc_final: 0.8309 (mmp) REVERT: B 840 ASP cc_start: 0.9108 (t0) cc_final: 0.8689 (t70) REVERT: B 881 PHE cc_start: 0.9054 (t80) cc_final: 0.8693 (t80) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2359 time to fit residues: 62.6053 Evaluate side-chains 139 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11890 Z= 0.169 Angle : 0.623 8.592 16094 Z= 0.311 Chirality : 0.042 0.188 1774 Planarity : 0.004 0.045 2020 Dihedral : 4.395 19.738 1562 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.58 (0.24), residues: 1398 helix: 2.11 (0.18), residues: 836 sheet: -1.48 (0.80), residues: 48 loop : -2.54 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.002 0.001 HIS A 402 PHE 0.018 0.001 PHE B 712 TYR 0.022 0.001 TYR A 687 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.8975 (t80) cc_final: 0.8733 (t80) REVERT: A 222 TYR cc_start: 0.9316 (p90) cc_final: 0.8988 (p90) REVERT: A 252 GLU cc_start: 0.9495 (tp30) cc_final: 0.9176 (tp30) REVERT: A 341 MET cc_start: 0.9263 (tpp) cc_final: 0.8876 (tpp) REVERT: A 367 MET cc_start: 0.9021 (mtt) cc_final: 0.8344 (mtt) REVERT: A 368 GLU cc_start: 0.9190 (mp0) cc_final: 0.8783 (mp0) REVERT: A 369 MET cc_start: 0.8913 (mmm) cc_final: 0.8599 (mpp) REVERT: A 461 ARG cc_start: 0.7224 (ttm170) cc_final: 0.6956 (tmt170) REVERT: A 702 GLU cc_start: 0.8326 (tp30) cc_final: 0.7422 (tp30) REVERT: A 734 GLU cc_start: 0.9167 (tp30) cc_final: 0.8501 (tp30) REVERT: A 738 ASP cc_start: 0.8323 (m-30) cc_final: 0.7353 (m-30) REVERT: A 755 LYS cc_start: 0.9295 (ptmm) cc_final: 0.8857 (ptpp) REVERT: A 756 ASP cc_start: 0.9338 (t0) cc_final: 0.9097 (m-30) REVERT: A 840 ASP cc_start: 0.9121 (t0) cc_final: 0.8706 (t70) REVERT: A 881 PHE cc_start: 0.9042 (t80) cc_final: 0.8673 (t80) REVERT: B 126 PHE cc_start: 0.8970 (t80) cc_final: 0.8749 (t80) REVERT: B 201 ILE cc_start: 0.8780 (tp) cc_final: 0.7929 (tp) REVERT: B 222 TYR cc_start: 0.9241 (p90) cc_final: 0.8881 (p90) REVERT: B 252 GLU cc_start: 0.9547 (tp30) cc_final: 0.9249 (tp30) REVERT: B 342 LEU cc_start: 0.9929 (mt) cc_final: 0.9669 (tp) REVERT: B 367 MET cc_start: 0.9363 (mtm) cc_final: 0.8902 (mtt) REVERT: B 368 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9150 (mm-30) REVERT: B 416 MET cc_start: 0.9358 (mmt) cc_final: 0.9086 (tpp) REVERT: B 461 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6942 (tmt170) REVERT: B 702 GLU cc_start: 0.8251 (tp30) cc_final: 0.7623 (tp30) REVERT: B 705 GLU cc_start: 0.8962 (pm20) cc_final: 0.8658 (pm20) REVERT: B 734 GLU cc_start: 0.9199 (tp30) cc_final: 0.8504 (tp30) REVERT: B 738 ASP cc_start: 0.8358 (m-30) cc_final: 0.7363 (m-30) REVERT: B 755 LYS cc_start: 0.9278 (ptmm) cc_final: 0.8892 (ptpp) REVERT: B 794 MET cc_start: 0.8560 (mmp) cc_final: 0.8307 (mmp) REVERT: B 840 ASP cc_start: 0.9106 (t0) cc_final: 0.8713 (t70) REVERT: B 881 PHE cc_start: 0.9039 (t80) cc_final: 0.8653 (t80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2333 time to fit residues: 62.5206 Evaluate side-chains 144 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.0170 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11890 Z= 0.152 Angle : 0.624 8.508 16094 Z= 0.310 Chirality : 0.042 0.182 1774 Planarity : 0.004 0.044 2020 Dihedral : 4.357 18.795 1562 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.61 (0.24), residues: 1398 helix: 2.10 (0.18), residues: 834 sheet: -1.40 (0.79), residues: 48 loop : -2.45 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 760 HIS 0.005 0.000 HIS B 453 PHE 0.015 0.001 PHE A 505 TYR 0.020 0.001 TYR A 687 ARG 0.004 0.000 ARG A 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.9007 (t80) cc_final: 0.8715 (t80) REVERT: A 222 TYR cc_start: 0.9301 (p90) cc_final: 0.8955 (p90) REVERT: A 252 GLU cc_start: 0.9507 (tp30) cc_final: 0.9165 (tp30) REVERT: A 341 MET cc_start: 0.9268 (tpp) cc_final: 0.8840 (tpp) REVERT: A 367 MET cc_start: 0.8980 (mtt) cc_final: 0.8327 (mtt) REVERT: A 368 GLU cc_start: 0.9187 (mp0) cc_final: 0.8747 (mp0) REVERT: A 369 MET cc_start: 0.8951 (mmm) cc_final: 0.8632 (mpp) REVERT: A 461 ARG cc_start: 0.7210 (ttm170) cc_final: 0.7003 (tmt170) REVERT: A 702 GLU cc_start: 0.8175 (tp30) cc_final: 0.7392 (tp30) REVERT: A 705 GLU cc_start: 0.8918 (pm20) cc_final: 0.8589 (pm20) REVERT: A 734 GLU cc_start: 0.9140 (tp30) cc_final: 0.8550 (tp30) REVERT: A 738 ASP cc_start: 0.8328 (m-30) cc_final: 0.7502 (m-30) REVERT: A 755 LYS cc_start: 0.9212 (ptmm) cc_final: 0.8761 (ptpp) REVERT: A 756 ASP cc_start: 0.9343 (t0) cc_final: 0.9089 (m-30) REVERT: A 840 ASP cc_start: 0.9070 (t0) cc_final: 0.8687 (t70) REVERT: A 881 PHE cc_start: 0.9030 (t80) cc_final: 0.8630 (t80) REVERT: B 126 PHE cc_start: 0.8971 (t80) cc_final: 0.8720 (t80) REVERT: B 222 TYR cc_start: 0.9234 (p90) cc_final: 0.8854 (p90) REVERT: B 252 GLU cc_start: 0.9540 (tp30) cc_final: 0.9234 (tp30) REVERT: B 342 LEU cc_start: 0.9891 (mt) cc_final: 0.9622 (tp) REVERT: B 367 MET cc_start: 0.9389 (mtm) cc_final: 0.8944 (mtt) REVERT: B 368 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9187 (mm-30) REVERT: B 461 ARG cc_start: 0.7200 (ttm170) cc_final: 0.6950 (tmt170) REVERT: B 499 PHE cc_start: 0.9031 (t80) cc_final: 0.8795 (t80) REVERT: B 702 GLU cc_start: 0.8217 (tp30) cc_final: 0.7634 (tp30) REVERT: B 705 GLU cc_start: 0.9001 (pm20) cc_final: 0.8640 (pm20) REVERT: B 734 GLU cc_start: 0.9157 (tp30) cc_final: 0.8560 (tp30) REVERT: B 738 ASP cc_start: 0.8275 (m-30) cc_final: 0.7532 (m-30) REVERT: B 755 LYS cc_start: 0.9260 (ptmm) cc_final: 0.8887 (ptpp) REVERT: B 794 MET cc_start: 0.8601 (mmp) cc_final: 0.8340 (mmp) REVERT: B 840 ASP cc_start: 0.9060 (t0) cc_final: 0.8680 (t70) REVERT: B 881 PHE cc_start: 0.9040 (t80) cc_final: 0.8654 (t80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2321 time to fit residues: 65.2796 Evaluate side-chains 154 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 709 GLN ** B 206 GLN ** 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 = 0.3344 r_free = 0.3344 target = 0.078136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.060890 restraints weight = 44283.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062526 restraints weight = 24415.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063571 restraints weight = 16660.423| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11890 Z= 0.165 Angle : 0.627 9.231 16094 Z= 0.311 Chirality : 0.042 0.181 1774 Planarity : 0.004 0.045 2020 Dihedral : 4.280 18.543 1562 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.67 (0.24), residues: 1398 helix: 2.14 (0.18), residues: 834 sheet: -1.36 (0.78), residues: 48 loop : -2.40 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 427 HIS 0.002 0.001 HIS B 402 PHE 0.018 0.001 PHE A 712 TYR 0.019 0.001 TYR B 687 ARG 0.004 0.000 ARG A 753 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.86 seconds wall clock time: 42 minutes 3.40 seconds (2523.40 seconds total)