Starting phenix.real_space_refine on Mon Mar 11 16:00:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m71_30127/03_2024/6m71_30127.pdb" } resolution = 2.9 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= 0.001 sd= 0.063 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 63 5.16 5 C 5507 2.51 5 N 1436 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A ASP 879": "OD1" <-> "OD2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6903 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 538 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 315 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 858 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.79, per 1000 atoms: 0.56 Number of scatterers: 8614 At special positions: 0 Unit cell: (88.56, 95.12, 117.26, 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 63 16.00 O 1608 8.00 N 1436 7.00 C 5507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.71 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 645 " distance=2.76 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 51.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.591A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.402A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.532A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.729A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.605A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.120A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.684A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.573A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.921A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.823A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.682A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.350A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.511A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.597A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.581A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 867 removed outlier: 4.004A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.602A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.772A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.508A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.573A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.133A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.512A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.052A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.158A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 560 removed outlier: 7.004A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 189 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 155 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.918A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821 393 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2765 1.34 - 1.46: 1748 1.46 - 1.58: 4196 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8805 Sorted by residual: bond pdb=" CA LEU A 931 " pdb=" C LEU A 931 " ideal model delta sigma weight residual 1.527 1.485 0.042 1.41e-02 5.03e+03 8.83e+00 bond pdb=" N VAL A 930 " pdb=" CA VAL A 930 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.34e+00 bond pdb=" N THR A 929 " pdb=" CA THR A 929 " ideal model delta sigma weight residual 1.466 1.431 0.034 1.51e-02 4.39e+03 5.21e+00 bond pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.93e+00 bond pdb=" C PRO A 927 " pdb=" N HIS A 928 " ideal model delta sigma weight residual 1.332 1.308 0.023 1.53e-02 4.27e+03 2.36e+00 ... (remaining 8800 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.56: 210 106.56 - 113.43: 4804 113.43 - 120.31: 3267 120.31 - 127.19: 3594 127.19 - 134.06: 81 Bond angle restraints: 11956 Sorted by residual: angle pdb=" N VAL A 495 " pdb=" CA VAL A 495 " pdb=" C VAL A 495 " ideal model delta sigma weight residual 107.98 118.88 -10.90 1.51e+00 4.39e-01 5.21e+01 angle pdb=" N VAL A 930 " pdb=" CA VAL A 930 " pdb=" C VAL A 930 " ideal model delta sigma weight residual 109.34 123.51 -14.17 2.08e+00 2.31e-01 4.64e+01 angle pdb=" N ASN A 497 " pdb=" CA ASN A 497 " pdb=" C ASN A 497 " ideal model delta sigma weight residual 111.02 115.22 -4.20 1.25e+00 6.40e-01 1.13e+01 angle pdb=" N THR A 929 " pdb=" CA THR A 929 " pdb=" C THR A 929 " ideal model delta sigma weight residual 107.67 100.79 6.88 2.09e+00 2.29e-01 1.08e+01 angle pdb=" C THR A 929 " pdb=" CA THR A 929 " pdb=" CB THR A 929 " ideal model delta sigma weight residual 112.09 107.64 4.45 1.43e+00 4.89e-01 9.68e+00 ... (remaining 11951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4794 17.96 - 35.93: 373 35.93 - 53.89: 55 53.89 - 71.85: 12 71.85 - 89.82: 4 Dihedral angle restraints: 5238 sinusoidal: 2021 harmonic: 3217 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C VAL A 930 " pdb=" N VAL A 930 " pdb=" CA VAL A 930 " pdb=" CB VAL A 930 " ideal model delta harmonic sigma weight residual -122.00 -133.00 11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sinusoidal sigma weight residual 93.00 56.68 36.32 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1286 0.088 - 0.176: 63 0.176 - 0.264: 3 0.264 - 0.352: 1 0.352 - 0.440: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA VAL A 930 " pdb=" N VAL A 930 " pdb=" C VAL A 930 " pdb=" CB VAL A 930 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASN A 497 " pdb=" N ASN A 497 " pdb=" C ASN A 497 " pdb=" CB ASN A 497 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA VAL A 495 " pdb=" N VAL A 495 " pdb=" C VAL A 495 " pdb=" CB VAL A 495 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1351 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 305 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ARG A 305 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 305 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS A 306 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A 232 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 339 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.022 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 69 2.55 - 3.14: 6939 3.14 - 3.73: 13228 3.73 - 4.31: 19144 4.31 - 4.90: 31839 Nonbonded interactions: 71219 Sorted by model distance: nonbonded pdb=" O VAL A 335 " pdb=" OD1 ASP A 336 " model vdw 1.966 3.040 nonbonded pdb=" O PHE A 506 " pdb=" OH TYR A 515 " model vdw 2.216 2.440 nonbonded pdb=" O PRO A 412 " pdb=" OH TYR A 546 " model vdw 2.219 2.440 nonbonded pdb=" O THR A 929 " pdb=" OG1 THR A 929 " model vdw 2.246 2.440 nonbonded pdb=" O ASN A 705 " pdb=" OG SER A 709 " model vdw 2.256 2.440 ... (remaining 71214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.570 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: 6.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.440 Find NCS groups from input model: 0.220 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.003 0.042 8805 Z= 0.204 Angle : 0.592 14.168 11956 Z= 0.356 Chirality : 0.045 0.440 1354 Planarity : 0.004 0.046 1522 Dihedral : 13.419 89.815 3150 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -3.06 (0.22), residues: 1065 helix: -1.49 (0.20), residues: 511 sheet: -1.80 (0.41), residues: 107 loop : -2.65 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 154 HIS 0.004 0.001 HIS A 439 PHE 0.016 0.001 PHE A 652 TYR 0.018 0.001 TYR A 788 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: C 3 MET cc_start: 0.6852 (tpp) cc_final: 0.6638 (tpp) REVERT: C 52 MET cc_start: 0.8261 (tpp) cc_final: 0.7208 (tmm) REVERT: D 101 ASP cc_start: 0.8004 (p0) cc_final: 0.7582 (p0) REVERT: B 156 ILE cc_start: 0.7742 (pt) cc_final: 0.7531 (pt) REVERT: B 168 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6509 (mp-120) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 1.0797 time to fit residues: 196.9224 Evaluate side-chains 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 414 ASN A 572 HIS A 599 HIS A 613 HIS A 773 GLN A 892 HIS C 18 GLN C 36 HIS D 100 ASN D 105 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 140 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8805 Z= 0.175 Angle : 0.518 7.476 11956 Z= 0.277 Chirality : 0.042 0.204 1354 Planarity : 0.004 0.037 1522 Dihedral : 4.392 22.173 1176 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.33 % Allowed : 12.80 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.40 (0.24), residues: 1065 helix: 0.13 (0.23), residues: 510 sheet: -1.28 (0.42), residues: 103 loop : -2.06 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 154 HIS 0.003 0.001 HIS A 650 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 0.888 Fit side-chains REVERT: A 658 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: C 5 ASP cc_start: 0.5636 (OUTLIER) cc_final: 0.5412 (t0) REVERT: C 47 GLU cc_start: 0.6846 (mp0) cc_final: 0.6612 (mp0) REVERT: D 101 ASP cc_start: 0.7924 (p0) cc_final: 0.7494 (p0) outliers start: 22 outliers final: 7 residues processed: 149 average time/residue: 0.9769 time to fit residues: 157.4620 Evaluate side-chains 133 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain C residue 5 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 613 HIS C 18 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8805 Z= 0.232 Angle : 0.533 7.198 11956 Z= 0.283 Chirality : 0.043 0.212 1354 Planarity : 0.003 0.038 1522 Dihedral : 4.424 24.247 1176 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.96 % Allowed : 14.92 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.86 (0.25), residues: 1065 helix: 0.53 (0.24), residues: 504 sheet: -1.13 (0.48), residues: 82 loop : -1.68 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 154 HIS 0.003 0.001 HIS A 816 PHE 0.017 0.002 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7978 (mp) REVERT: A 658 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: A 882 HIS cc_start: 0.7104 (m-70) cc_final: 0.6776 (m170) REVERT: C 3 MET cc_start: 0.6053 (tpp) cc_final: 0.5715 (tpp) REVERT: C 47 GLU cc_start: 0.6858 (mp0) cc_final: 0.6635 (mp0) REVERT: D 101 ASP cc_start: 0.7972 (p0) cc_final: 0.7551 (p0) REVERT: B 154 TRP cc_start: 0.7612 (OUTLIER) cc_final: 0.7160 (m100) outliers start: 28 outliers final: 15 residues processed: 158 average time/residue: 0.9737 time to fit residues: 166.8960 Evaluate side-chains 149 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 613 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8805 Z= 0.272 Angle : 0.549 7.025 11956 Z= 0.293 Chirality : 0.044 0.217 1354 Planarity : 0.004 0.037 1522 Dihedral : 4.497 24.998 1176 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.60 % Allowed : 14.71 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.70 (0.25), residues: 1065 helix: 0.65 (0.24), residues: 498 sheet: -1.09 (0.50), residues: 82 loop : -1.54 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 PHE 0.017 0.002 PHE A 741 TYR 0.020 0.002 TYR A 420 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.8026 (tp) cc_final: 0.7712 (tp) REVERT: A 372 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7962 (mp) REVERT: A 658 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: A 882 HIS cc_start: 0.7113 (m-70) cc_final: 0.6797 (m170) REVERT: D 101 ASP cc_start: 0.7917 (p0) cc_final: 0.7515 (p0) REVERT: B 154 TRP cc_start: 0.7705 (OUTLIER) cc_final: 0.7455 (m100) outliers start: 34 outliers final: 17 residues processed: 154 average time/residue: 0.9095 time to fit residues: 152.4348 Evaluate side-chains 147 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8805 Z= 0.184 Angle : 0.508 7.242 11956 Z= 0.269 Chirality : 0.041 0.157 1354 Planarity : 0.003 0.036 1522 Dihedral : 4.285 22.396 1176 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.39 % Allowed : 16.08 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.36 (0.25), residues: 1065 helix: 0.88 (0.24), residues: 498 sheet: -0.88 (0.52), residues: 82 loop : -1.31 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.023 0.001 TYR A 420 ARG 0.001 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.7926 (tp) cc_final: 0.7609 (tp) REVERT: A 372 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 658 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: A 662 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8707 (p) REVERT: A 818 MET cc_start: 0.6211 (ptt) cc_final: 0.5806 (pmt) REVERT: A 882 HIS cc_start: 0.7110 (m-70) cc_final: 0.6783 (m170) REVERT: D 101 ASP cc_start: 0.7924 (p0) cc_final: 0.7579 (p0) REVERT: B 154 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.6710 (m100) outliers start: 32 outliers final: 19 residues processed: 154 average time/residue: 0.8675 time to fit residues: 145.8916 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.0570 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8805 Z= 0.260 Angle : 0.548 7.253 11956 Z= 0.290 Chirality : 0.043 0.153 1354 Planarity : 0.003 0.038 1522 Dihedral : 4.415 24.598 1176 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.92 % Allowed : 17.46 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.39 (0.25), residues: 1065 helix: 0.82 (0.24), residues: 500 sheet: -0.85 (0.53), residues: 82 loop : -1.29 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 154 HIS 0.004 0.001 HIS C 36 PHE 0.018 0.002 PHE A 741 TYR 0.026 0.001 TYR A 420 ARG 0.001 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.7983 (tp) cc_final: 0.7682 (tp) REVERT: A 658 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: A 662 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8691 (p) REVERT: A 818 MET cc_start: 0.6255 (ptt) cc_final: 0.5860 (pmt) REVERT: A 882 HIS cc_start: 0.7130 (m-70) cc_final: 0.6797 (m170) REVERT: D 101 ASP cc_start: 0.7934 (p0) cc_final: 0.7612 (p0) REVERT: B 154 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.7356 (m100) outliers start: 37 outliers final: 19 residues processed: 154 average time/residue: 0.8951 time to fit residues: 150.3671 Evaluate side-chains 149 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8805 Z= 0.174 Angle : 0.524 7.535 11956 Z= 0.276 Chirality : 0.042 0.152 1354 Planarity : 0.003 0.042 1522 Dihedral : 4.216 21.304 1176 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.17 % Allowed : 18.20 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.05 (0.26), residues: 1065 helix: 1.06 (0.24), residues: 497 sheet: -0.68 (0.54), residues: 82 loop : -1.07 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.025 0.001 TYR A 420 ARG 0.001 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.006 Fit side-chains REVERT: A 241 LEU cc_start: 0.7916 (tp) cc_final: 0.7615 (tp) REVERT: A 658 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: A 662 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8739 (p) REVERT: A 818 MET cc_start: 0.6195 (ptt) cc_final: 0.5796 (pmt) REVERT: A 882 HIS cc_start: 0.7071 (m-70) cc_final: 0.6802 (m170) REVERT: D 101 ASP cc_start: 0.7898 (p0) cc_final: 0.7616 (p0) REVERT: B 154 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.6457 (m100) REVERT: B 174 MET cc_start: 0.7493 (tmm) cc_final: 0.7052 (tpp) outliers start: 30 outliers final: 14 residues processed: 148 average time/residue: 1.0245 time to fit residues: 165.0954 Evaluate side-chains 140 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8805 Z= 0.170 Angle : 0.533 8.313 11956 Z= 0.276 Chirality : 0.042 0.153 1354 Planarity : 0.003 0.052 1522 Dihedral : 4.142 21.086 1176 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 19.05 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.07 (0.26), residues: 1065 helix: 1.14 (0.24), residues: 496 sheet: -0.53 (0.51), residues: 92 loop : -0.99 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.026 0.001 TYR A 420 ARG 0.001 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.041 Fit side-chains REVERT: A 241 LEU cc_start: 0.7910 (tp) cc_final: 0.7601 (tp) REVERT: A 340 PHE cc_start: 0.7013 (m-80) cc_final: 0.6764 (m-80) REVERT: A 662 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 818 MET cc_start: 0.6197 (ptt) cc_final: 0.5779 (pmt) REVERT: A 882 HIS cc_start: 0.7059 (m-70) cc_final: 0.6754 (m170) REVERT: C 51 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7911 (mtmt) REVERT: D 101 ASP cc_start: 0.7889 (p0) cc_final: 0.7606 (p0) REVERT: B 154 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6205 (m100) REVERT: B 174 MET cc_start: 0.7491 (tmm) cc_final: 0.7032 (tpp) outliers start: 24 outliers final: 14 residues processed: 146 average time/residue: 0.9382 time to fit residues: 149.7056 Evaluate side-chains 140 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8805 Z= 0.164 Angle : 0.538 7.433 11956 Z= 0.280 Chirality : 0.042 0.152 1354 Planarity : 0.003 0.059 1522 Dihedral : 4.100 20.819 1176 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 19.79 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.23 (0.26), residues: 1065 helix: 1.24 (0.24), residues: 495 sheet: -0.46 (0.52), residues: 92 loop : -0.85 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.026 0.001 TYR A 420 ARG 0.001 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.881 Fit side-chains REVERT: A 241 LEU cc_start: 0.7881 (tp) cc_final: 0.7570 (tp) REVERT: A 372 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 818 MET cc_start: 0.6110 (ptt) cc_final: 0.5709 (pmt) REVERT: A 882 HIS cc_start: 0.7062 (m-70) cc_final: 0.6811 (m170) REVERT: C 15 SER cc_start: 0.8250 (t) cc_final: 0.8018 (m) REVERT: D 101 ASP cc_start: 0.7908 (p0) cc_final: 0.7626 (p0) REVERT: B 154 TRP cc_start: 0.7371 (OUTLIER) cc_final: 0.6212 (m100) REVERT: B 174 MET cc_start: 0.7454 (tmm) cc_final: 0.7168 (tpp) outliers start: 24 outliers final: 15 residues processed: 142 average time/residue: 0.8900 time to fit residues: 138.1005 Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8805 Z= 0.313 Angle : 0.618 7.783 11956 Z= 0.326 Chirality : 0.045 0.159 1354 Planarity : 0.004 0.062 1522 Dihedral : 4.560 27.855 1176 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.43 % Allowed : 20.63 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.33 (0.25), residues: 1065 helix: 0.66 (0.23), residues: 514 sheet: -0.68 (0.56), residues: 82 loop : -1.08 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 154 HIS 0.005 0.001 HIS C 36 PHE 0.019 0.002 PHE A 741 TYR 0.029 0.002 TYR A 420 ARG 0.002 0.000 ARG A 654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.983 Fit side-chains REVERT: A 241 LEU cc_start: 0.8036 (tp) cc_final: 0.7750 (tp) REVERT: A 818 MET cc_start: 0.6261 (ptt) cc_final: 0.5875 (pmt) REVERT: A 882 HIS cc_start: 0.7151 (m-70) cc_final: 0.6844 (m170) REVERT: D 101 ASP cc_start: 0.7914 (p0) cc_final: 0.7576 (p0) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.8837 time to fit residues: 132.1639 Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119889 restraints weight = 13702.213| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.06 r_work: 0.3522 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8805 Z= 0.154 Angle : 0.548 9.454 11956 Z= 0.284 Chirality : 0.041 0.156 1354 Planarity : 0.003 0.063 1522 Dihedral : 4.118 20.197 1176 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.90 % Allowed : 21.38 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.23 (0.26), residues: 1065 helix: 1.21 (0.24), residues: 495 sheet: -0.49 (0.52), residues: 95 loop : -0.80 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 154 HIS 0.003 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.024 0.001 TYR A 420 ARG 0.001 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.65 seconds wall clock time: 57 minutes 26.46 seconds (3446.46 seconds total)