Starting phenix.real_space_refine on Wed Feb 14 02:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xj9_33222/02_2024/7xj9_33222.pdb" } resolution = 3.27 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= -0.003 sd= 0.028 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 39 5.16 5 C 5306 2.51 5 N 1423 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 104": "OD1" <-> "OD2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8375 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Time building chain proxies: 4.93, per 1000 atoms: 0.59 Number of scatterers: 8375 At special positions: 0 Unit cell: (96.76, 124.64, 114.8, 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 39 16.00 O 1607 8.00 N 1423 7.00 C 5306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 106 " distance=2.03 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.539A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.608A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.803A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.612A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.521A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.526A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.154A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.367A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.640A pdb=" N PHE J 84 " --> pdb=" O SER J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 31 removed outlier: 3.963A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 31' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.154A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.961A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.526A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.846A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.718A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 13 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.582A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.982A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.684A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.737A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.768A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 6 removed outlier: 4.014A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.279A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.623A pdb=" N ASP I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.907A pdb=" N THR J 75 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER J 64 " --> pdb=" O THR J 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.635A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.532A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 264 hydrogen bonds defined for protein. 591 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: 2.43 Time building geometry restraints manager: 3.33 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: 2679 1.34 - 1.46: 2195 1.46 - 1.58: 3662 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8584 Sorted by residual: bond pdb=" N SER K 55 " pdb=" CA SER K 55 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" N ASP K 108 " pdb=" CA ASP K 108 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.82e+00 bond pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.30e-02 5.92e+03 4.14e+00 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.35e-02 5.49e+03 3.68e+00 bond pdb=" N LYS B 478 " pdb=" CA LYS B 478 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.64e-02 3.72e+03 3.34e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.10: 194 106.10 - 113.08: 4433 113.08 - 120.05: 2931 120.05 - 127.02: 4003 127.02 - 133.99: 93 Bond angle restraints: 11654 Sorted by residual: angle pdb=" N ASN B 487 " pdb=" CA ASN B 487 " pdb=" C ASN B 487 " ideal model delta sigma weight residual 113.23 107.46 5.77 1.22e+00 6.72e-01 2.23e+01 angle pdb=" CA PRO C 521 " pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.19e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 123.47 118.46 5.01 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N GLY J 16 " pdb=" CA GLY J 16 " pdb=" C GLY J 16 " ideal model delta sigma weight residual 114.92 110.74 4.18 1.30e+00 5.92e-01 1.03e+01 angle pdb=" CB ARG K 87 " pdb=" CG ARG K 87 " pdb=" CD ARG K 87 " ideal model delta sigma weight residual 111.30 116.74 -5.44 2.30e+00 1.89e-01 5.60e+00 ... (remaining 11649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4621 17.73 - 35.45: 394 35.45 - 53.18: 51 53.18 - 70.91: 3 70.91 - 88.63: 10 Dihedral angle restraints: 5079 sinusoidal: 1973 harmonic: 3106 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.16 -71.16 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 133.17 -40.17 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 836 0.037 - 0.074: 283 0.074 - 0.111: 109 0.111 - 0.148: 28 0.148 - 0.185: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CG LEU J 34 " pdb=" CB LEU J 34 " pdb=" CD1 LEU J 34 " pdb=" CD2 LEU J 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CB THR J 20 " pdb=" CA THR J 20 " pdb=" OG1 THR J 20 " pdb=" CG2 THR J 20 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE H 106 " pdb=" N ILE H 106 " pdb=" C ILE H 106 " pdb=" CB ILE H 106 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1254 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 8 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO K 9 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO K 9 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 9 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.054 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO C 521 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 87 " 0.133 9.50e-02 1.11e+02 6.00e-02 2.84e+00 pdb=" NE ARG K 87 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG K 87 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 87 " 0.000 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 166 2.68 - 3.23: 7588 3.23 - 3.79: 11877 3.79 - 4.34: 16550 4.34 - 4.90: 28169 Nonbonded interactions: 64350 Sorted by model distance: nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.122 2.440 nonbonded pdb=" O TYR J 50 " pdb=" OG SER J 54 " model vdw 2.159 2.440 nonbonded pdb=" OG SER I 17 " pdb=" OE2 GLU I 82 " model vdw 2.191 2.440 nonbonded pdb=" OD1 ASP H 17 " pdb=" N ARG H 18 " model vdw 2.202 2.520 nonbonded pdb=" OG SER F 63 " pdb=" OG1 THR F 74 " model vdw 2.204 2.440 ... (remaining 64345 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 'B' selection = (chain 'C' and resid 335 through 527) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 6.360 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: 27.450 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 26.320 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 0.070 8584 Z= 0.202 Angle : 0.573 6.375 11654 Z= 0.317 Chirality : 0.044 0.185 1257 Planarity : 0.005 0.088 1498 Dihedral : 12.826 88.633 3060 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.12 (0.26), residues: 1058 helix: -4.33 (0.43), residues: 48 sheet: -0.21 (0.26), residues: 438 loop : -0.78 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 47 HIS 0.004 0.001 HIS K 107 PHE 0.013 0.001 PHE F 83 TYR 0.013 0.001 TYR J 37 ARG 0.014 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 2 MET cc_start: 0.5927 (ptt) cc_final: 0.5657 (ptt) REVERT: K 81 MET cc_start: 0.7338 (tmm) cc_final: 0.6758 (tmm) REVERT: K 118 VAL cc_start: 0.8334 (t) cc_final: 0.8126 (m) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2231 time to fit residues: 57.8524 Evaluate side-chains 158 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8584 Z= 0.176 Angle : 0.542 6.891 11654 Z= 0.286 Chirality : 0.045 0.144 1257 Planarity : 0.004 0.059 1498 Dihedral : 4.175 14.423 1185 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.53 % Allowed : 9.40 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.90 (0.26), residues: 1058 helix: -4.02 (0.52), residues: 49 sheet: -0.01 (0.27), residues: 417 loop : -0.67 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.003 0.001 HIS C 505 PHE 0.011 0.001 PHE F 83 TYR 0.014 0.001 TYR J 50 ARG 0.007 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4908 (mtmt) REVERT: H 6 GLN cc_start: 0.8263 (mt0) cc_final: 0.8045 (mt0) REVERT: K 81 MET cc_start: 0.7527 (tmm) cc_final: 0.6846 (tmm) outliers start: 14 outliers final: 10 residues processed: 184 average time/residue: 0.2161 time to fit residues: 53.6077 Evaluate side-chains 180 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8584 Z= 0.167 Angle : 0.526 6.807 11654 Z= 0.276 Chirality : 0.044 0.141 1257 Planarity : 0.004 0.047 1498 Dihedral : 4.048 14.297 1185 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.86 % Allowed : 11.58 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.84 (0.26), residues: 1058 helix: -3.86 (0.62), residues: 42 sheet: 0.05 (0.27), residues: 407 loop : -0.70 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.013 0.001 HIS K 107 PHE 0.018 0.001 PHE K 27 TYR 0.015 0.001 TYR J 50 ARG 0.008 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.7830 (t0) cc_final: 0.6997 (t0) REVERT: J 50 TYR cc_start: 0.5529 (p90) cc_final: 0.5325 (p90) REVERT: K 81 MET cc_start: 0.7611 (tmm) cc_final: 0.6924 (tmm) REVERT: K 95 TYR cc_start: 0.7299 (m-80) cc_final: 0.6803 (m-80) outliers start: 17 outliers final: 14 residues processed: 199 average time/residue: 0.2098 time to fit residues: 56.7412 Evaluate side-chains 191 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8584 Z= 0.272 Angle : 0.580 7.125 11654 Z= 0.304 Chirality : 0.046 0.165 1257 Planarity : 0.004 0.041 1498 Dihedral : 4.385 16.906 1185 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.93 % Allowed : 11.58 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.96 (0.26), residues: 1058 helix: -3.84 (0.62), residues: 42 sheet: -0.06 (0.27), residues: 413 loop : -0.76 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 36 HIS 0.009 0.001 HIS K 107 PHE 0.014 0.001 PHE K 27 TYR 0.013 0.001 TYR F 91 ARG 0.008 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 25 SER cc_start: 0.7299 (t) cc_final: 0.7081 (m) REVERT: K 81 MET cc_start: 0.7812 (tmm) cc_final: 0.6919 (tmm) outliers start: 36 outliers final: 25 residues processed: 194 average time/residue: 0.2129 time to fit residues: 56.0730 Evaluate side-chains 196 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8584 Z= 0.212 Angle : 0.560 7.545 11654 Z= 0.293 Chirality : 0.045 0.252 1257 Planarity : 0.004 0.038 1498 Dihedral : 4.279 15.148 1185 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.83 % Allowed : 12.68 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.94 (0.26), residues: 1058 helix: -3.86 (0.62), residues: 42 sheet: -0.04 (0.27), residues: 410 loop : -0.76 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.007 0.001 HIS K 107 PHE 0.021 0.001 PHE K 27 TYR 0.010 0.001 TYR H 49 ARG 0.010 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: K 25 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.7054 (m) REVERT: K 81 MET cc_start: 0.7799 (tmm) cc_final: 0.6863 (tmm) outliers start: 35 outliers final: 29 residues processed: 196 average time/residue: 0.2171 time to fit residues: 57.0954 Evaluate side-chains 204 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8584 Z= 0.196 Angle : 0.550 7.764 11654 Z= 0.286 Chirality : 0.044 0.186 1257 Planarity : 0.004 0.045 1498 Dihedral : 4.192 15.065 1185 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.61 % Allowed : 13.66 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.97 (0.26), residues: 1058 helix: -3.87 (0.61), residues: 42 sheet: -0.05 (0.27), residues: 411 loop : -0.79 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS K 107 PHE 0.022 0.001 PHE K 27 TYR 0.011 0.001 TYR J 37 ARG 0.012 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 12 LYS cc_start: 0.7282 (mmmm) cc_final: 0.7047 (mmtp) REVERT: K 25 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7149 (m) REVERT: K 81 MET cc_start: 0.7707 (tmm) cc_final: 0.6828 (tmm) outliers start: 33 outliers final: 28 residues processed: 193 average time/residue: 0.2301 time to fit residues: 60.1358 Evaluate side-chains 203 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8584 Z= 0.246 Angle : 0.582 8.058 11654 Z= 0.304 Chirality : 0.045 0.209 1257 Planarity : 0.004 0.048 1498 Dihedral : 4.371 16.032 1185 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.72 % Allowed : 14.10 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.05 (0.26), residues: 1058 helix: -3.86 (0.61), residues: 42 sheet: -0.10 (0.27), residues: 411 loop : -0.85 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.006 0.001 HIS K 107 PHE 0.023 0.001 PHE K 27 TYR 0.012 0.001 TYR F 91 ARG 0.012 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 25 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7142 (m) REVERT: K 81 MET cc_start: 0.7630 (tmm) cc_final: 0.6750 (tmm) outliers start: 34 outliers final: 32 residues processed: 193 average time/residue: 0.2423 time to fit residues: 63.5413 Evaluate side-chains 202 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8584 Z= 0.208 Angle : 0.569 9.033 11654 Z= 0.295 Chirality : 0.045 0.218 1257 Planarity : 0.004 0.053 1498 Dihedral : 4.289 16.080 1185 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.72 % Allowed : 14.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.11 (0.26), residues: 1058 helix: -4.07 (0.55), residues: 48 sheet: -0.10 (0.27), residues: 410 loop : -0.87 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 47 HIS 0.006 0.001 HIS K 107 PHE 0.025 0.001 PHE K 27 TYR 0.013 0.001 TYR I 32 ARG 0.012 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 25 SER cc_start: 0.7446 (OUTLIER) cc_final: 0.7185 (m) REVERT: K 81 MET cc_start: 0.7657 (tmm) cc_final: 0.6767 (tmm) outliers start: 34 outliers final: 30 residues processed: 187 average time/residue: 0.2208 time to fit residues: 56.0113 Evaluate side-chains 200 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8584 Z= 0.145 Angle : 0.544 9.154 11654 Z= 0.280 Chirality : 0.044 0.195 1257 Planarity : 0.004 0.055 1498 Dihedral : 3.999 14.683 1185 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.84 % Allowed : 15.74 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.02 (0.26), residues: 1058 helix: -4.10 (0.54), residues: 48 sheet: 0.05 (0.27), residues: 403 loop : -0.86 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 113 HIS 0.005 0.001 HIS K 107 PHE 0.026 0.001 PHE K 27 TYR 0.008 0.001 TYR J 37 ARG 0.014 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8323 (t) REVERT: K 25 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7225 (m) REVERT: K 81 MET cc_start: 0.7603 (tmm) cc_final: 0.6745 (tmm) outliers start: 26 outliers final: 22 residues processed: 194 average time/residue: 0.2215 time to fit residues: 57.8144 Evaluate side-chains 197 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.179 Angle : 0.552 8.803 11654 Z= 0.285 Chirality : 0.044 0.197 1257 Planarity : 0.004 0.041 1498 Dihedral : 4.023 14.288 1185 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.73 % Allowed : 16.61 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.02 (0.26), residues: 1058 helix: -4.08 (0.55), residues: 48 sheet: -0.01 (0.27), residues: 405 loop : -0.82 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 113 HIS 0.005 0.001 HIS K 107 PHE 0.025 0.001 PHE K 27 TYR 0.013 0.001 TYR K 60 ARG 0.009 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8357 (t) REVERT: K 25 SER cc_start: 0.7510 (OUTLIER) cc_final: 0.7248 (m) REVERT: K 81 MET cc_start: 0.7570 (tmm) cc_final: 0.6699 (tmm) outliers start: 25 outliers final: 22 residues processed: 185 average time/residue: 0.2056 time to fit residues: 51.7629 Evaluate side-chains 192 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092450 restraints weight = 17454.314| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.17 r_work: 0.3267 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8584 Z= 0.161 Angle : 0.550 8.786 11654 Z= 0.283 Chirality : 0.044 0.183 1257 Planarity : 0.004 0.048 1498 Dihedral : 3.959 15.530 1185 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.95 % Allowed : 16.61 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.00 (0.26), residues: 1058 helix: -4.08 (0.55), residues: 48 sheet: 0.06 (0.27), residues: 402 loop : -0.85 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 113 HIS 0.005 0.001 HIS K 107 PHE 0.024 0.001 PHE K 27 TYR 0.011 0.001 TYR J 37 ARG 0.014 0.000 ARG K 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.02 seconds wall clock time: 46 minutes 30.38 seconds (2790.38 seconds total)