Starting phenix.real_space_refine on Mon Mar 11 08:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/03_2024/7fbi_31515.pdb" } resolution = 3.9 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= 0.002 sd= 0.906 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 4895 2.51 5 N 1310 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7777 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 812 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "A" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4467 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 540} Chain breaks: 3 Chain: "M" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 819 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 881 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Time building chain proxies: 4.66, per 1000 atoms: 0.60 Number of scatterers: 7777 At special positions: 0 Unit cell: (69.3, 158.4, 192.5, 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 1533 8.00 N 1310 7.00 C 4895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 93 " 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 20 sheets defined 9.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.165A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR H 32 " --> pdb=" O LEU H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.720A pdb=" N GLU A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.984A pdb=" N ILE A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.822A pdb=" N LYS A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 removed outlier: 3.919A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.633A pdb=" N CYS A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.196A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 645 through 651 removed outlier: 3.915A pdb=" N ARG A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.981A pdb=" N PHE A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG A 662 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.530A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN H 39 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.592A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 74 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.929A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.929A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.749A pdb=" N GLY A 80 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 306 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 311 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 314 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 125 removed outlier: 3.643A pdb=" N ASN A 105 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 94 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 213 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.661A pdb=" N ALA A 213 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 94 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 277 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 149 removed outlier: 4.072A pdb=" N VAL A 145 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 156 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 147 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 370 through 373 removed outlier: 3.796A pdb=" N THR A 370 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP A 382 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 372 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 552 Processing sheet with id=AB5, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.574A pdb=" N GLN A 571 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 579 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 594 through 598 removed outlier: 3.680A pdb=" N TYR A 594 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 605 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 596 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 603 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 601 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 612 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.675A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS M 23 " --> pdb=" O TYR M 71 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 67 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 35 through 38 removed outlier: 3.744A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG M 38 " --> pdb=" O THR M 85 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR M 85 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.592A pdb=" N THR N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL N 76 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP N 77 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 18 through 19 removed outlier: 3.571A pdb=" N MET N 80 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 33 through 39 removed outlier: 4.501A pdb=" N GLU N 33 " --> pdb=" O GLY N 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL N 37 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN N 39 " --> pdb=" O THR N 90 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 90 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR N 114 " --> pdb=" O TYR N 91 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 318 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: 2.03 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1273 1.31 - 1.44: 2253 1.44 - 1.57: 4352 1.57 - 1.70: 2 1.70 - 1.83: 58 Bond restraints: 7938 Sorted by residual: bond pdb=" N HIS A 352 " pdb=" CA HIS A 352 " ideal model delta sigma weight residual 1.459 1.375 0.085 1.18e-02 7.18e+03 5.16e+01 bond pdb=" CA ARG H 10 " pdb=" C ARG H 10 " ideal model delta sigma weight residual 1.523 1.598 -0.075 1.34e-02 5.57e+03 3.16e+01 bond pdb=" C SER M 93 " pdb=" O SER M 93 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" CA PHE M 92 " pdb=" C PHE M 92 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.12e-02 7.97e+03 2.02e+01 bond pdb=" C HIS A 352 " pdb=" N GLU A 353 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.27e-02 6.20e+03 1.92e+01 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.93: 164 105.93 - 112.99: 4134 112.99 - 120.05: 2759 120.05 - 127.10: 3618 127.10 - 134.16: 95 Bond angle restraints: 10770 Sorted by residual: angle pdb=" N SER M 95 " pdb=" CA SER M 95 " pdb=" C SER M 95 " ideal model delta sigma weight residual 109.24 127.19 -17.95 1.51e+00 4.39e-01 1.41e+02 angle pdb=" C MET A 351 " pdb=" N HIS A 352 " pdb=" CA HIS A 352 " ideal model delta sigma weight residual 120.63 108.66 11.97 1.36e+00 5.41e-01 7.75e+01 angle pdb=" N GLN M 90 " pdb=" CA GLN M 90 " pdb=" C GLN M 90 " ideal model delta sigma weight residual 112.59 122.19 -9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N GLY M 91 " pdb=" CA GLY M 91 " pdb=" C GLY M 91 " ideal model delta sigma weight residual 111.34 125.65 -14.31 1.82e+00 3.02e-01 6.18e+01 angle pdb=" N PHE M 92 " pdb=" CA PHE M 92 " pdb=" C PHE M 92 " ideal model delta sigma weight residual 110.70 120.15 -9.45 1.55e+00 4.16e-01 3.72e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4054 16.60 - 33.20: 500 33.20 - 49.79: 93 49.79 - 66.39: 19 66.39 - 82.99: 13 Dihedral angle restraints: 4679 sinusoidal: 1799 harmonic: 2880 Sorted by residual: dihedral pdb=" CA TRP N 47 " pdb=" C TRP N 47 " pdb=" N ILE N 48 " pdb=" CA ILE N 48 " ideal model delta harmonic sigma weight residual 180.00 -119.15 -60.85 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA TYR N 106 " pdb=" C TYR N 106 " pdb=" N PHE N 107 " pdb=" CA PHE N 107 " ideal model delta harmonic sigma weight residual 180.00 135.46 44.54 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" N SER M 95 " pdb=" C SER M 95 " pdb=" CA SER M 95 " pdb=" CB SER M 95 " ideal model delta harmonic sigma weight residual 122.80 143.24 -20.44 0 2.50e+00 1.60e-01 6.68e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 1206 0.202 - 0.404: 11 0.404 - 0.606: 2 0.606 - 0.807: 0 0.807 - 1.009: 1 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA SER M 95 " pdb=" N SER M 95 " pdb=" C SER M 95 " pdb=" CB SER M 95 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA ARG H 10 " pdb=" N ARG H 10 " pdb=" C ARG H 10 " pdb=" CB ARG H 10 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA GLN M 90 " pdb=" N GLN M 90 " pdb=" C GLN M 90 " pdb=" CB GLN M 90 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 1217 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 352 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C HIS A 352 " -0.069 2.00e-02 2.50e+03 pdb=" O HIS A 352 " 0.027 2.00e-02 2.50e+03 pdb=" N GLU A 353 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 91 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C GLY M 91 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY M 91 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE M 92 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN M 90 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" CD GLN M 90 " 0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN M 90 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN M 90 " -0.017 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 262 2.66 - 3.22: 6924 3.22 - 3.78: 11285 3.78 - 4.34: 13074 4.34 - 4.90: 21101 Nonbonded interactions: 52646 Sorted by model distance: nonbonded pdb=" O HIS A 352 " pdb=" N TYR A 355 " model vdw 2.095 2.520 nonbonded pdb=" OE1 GLN M 90 " pdb=" O SER M 100 " model vdw 2.102 3.040 nonbonded pdb=" OG SER M 95 " pdb=" N ASN M 96 " model vdw 2.198 2.520 nonbonded pdb=" N GLN M 90 " pdb=" OE1 GLN M 90 " model vdw 2.217 2.520 nonbonded pdb=" OH TYR A 142 " pdb=" OD1 ASN A 163 " model vdw 2.232 2.440 ... (remaining 52641 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 6.220 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.120 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 7938 Z= 0.451 Angle : 1.182 17.954 10770 Z= 0.659 Chirality : 0.073 1.009 1220 Planarity : 0.007 0.062 1374 Dihedral : 15.514 82.990 2841 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.56 % Favored : 85.34 % Rotamer: Outliers : 0.35 % Allowed : 14.67 % Favored : 84.98 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -5.16 (0.20), residues: 989 helix: -4.53 (0.26), residues: 67 sheet: -3.23 (0.29), residues: 255 loop : -3.61 (0.18), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP N 110 HIS 0.008 0.002 HIS A 603 PHE 0.030 0.002 PHE N 107 TYR 0.032 0.002 TYR M 87 ARG 0.008 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 0.905 Fit side-chains REVERT: H 5 LYS cc_start: 0.9268 (mmmt) cc_final: 0.9061 (mmmt) REVERT: H 29 LEU cc_start: 0.8711 (tt) cc_final: 0.8284 (mm) REVERT: H 79 LYS cc_start: 0.9147 (mmtp) cc_final: 0.8855 (mmtm) REVERT: H 101 MET cc_start: 0.8774 (mmm) cc_final: 0.8122 (mtt) REVERT: L 35 TRP cc_start: 0.7424 (m-10) cc_final: 0.6904 (m-10) REVERT: L 37 GLN cc_start: 0.9440 (tm-30) cc_final: 0.8951 (tm-30) REVERT: L 38 GLN cc_start: 0.9113 (pp30) cc_final: 0.8690 (pm20) REVERT: L 39 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8175 (tppt) REVERT: L 42 GLN cc_start: 0.8744 (mp10) cc_final: 0.8480 (mp10) REVERT: L 55 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7902 (tm-30) REVERT: L 63 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8032 (mtm110) REVERT: L 70 GLU cc_start: 0.8738 (pp20) cc_final: 0.8435 (mt-10) REVERT: L 78 LEU cc_start: 0.8804 (mm) cc_final: 0.8378 (mt) REVERT: L 101 ASN cc_start: 0.8794 (p0) cc_final: 0.8154 (p0) REVERT: A 125 PHE cc_start: 0.8635 (m-10) cc_final: 0.8105 (m-10) REVERT: A 147 MET cc_start: 0.7971 (tmm) cc_final: 0.7299 (tmm) REVERT: A 181 TYR cc_start: 0.7255 (m-80) cc_final: 0.7048 (m-80) REVERT: A 212 MET cc_start: 0.8189 (tpp) cc_final: 0.7910 (tpp) REVERT: A 256 ASN cc_start: 0.9171 (p0) cc_final: 0.8941 (p0) REVERT: A 272 GLU cc_start: 0.8672 (tp30) cc_final: 0.8079 (mt-10) REVERT: A 279 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8276 (mmmm) REVERT: A 313 LYS cc_start: 0.9362 (tppp) cc_final: 0.9033 (tppt) REVERT: A 344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7332 (mp0) REVERT: A 382 TRP cc_start: 0.6197 (p-90) cc_final: 0.5726 (p-90) REVERT: A 486 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 492 MET cc_start: 0.9320 (tmm) cc_final: 0.9105 (tmm) REVERT: A 568 TYR cc_start: 0.8213 (m-10) cc_final: 0.8004 (m-80) REVERT: A 589 GLN cc_start: 0.8418 (pm20) cc_final: 0.8188 (pm20) REVERT: A 600 ASN cc_start: 0.9005 (t0) cc_final: 0.8575 (t0) REVERT: A 603 HIS cc_start: 0.8715 (p-80) cc_final: 0.8481 (p-80) REVERT: A 609 HIS cc_start: 0.8156 (m90) cc_final: 0.7621 (m90) REVERT: A 635 ASN cc_start: 0.9020 (p0) cc_final: 0.8760 (m-40) REVERT: A 653 ASN cc_start: 0.8909 (t0) cc_final: 0.8258 (t0) REVERT: A 662 ARG cc_start: 0.8798 (ptm-80) cc_final: 0.7945 (ttm170) REVERT: A 663 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8398 (tm-30) REVERT: M 2 LEU cc_start: 0.8616 (pt) cc_final: 0.8386 (pp) REVERT: M 22 LYS cc_start: 0.8271 (pttt) cc_final: 0.8026 (ptpp) REVERT: M 88 CYS cc_start: 0.4654 (p) cc_final: 0.3653 (p) REVERT: M 92 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.3828 (t80) REVERT: N 22 CYS cc_start: 0.5443 (t) cc_final: 0.5185 (t) REVERT: N 32 TYR cc_start: 0.7378 (m-80) cc_final: 0.5917 (m-80) REVERT: N 34 MET cc_start: 0.9205 (mmp) cc_final: 0.8833 (mmp) REVERT: N 36 TRP cc_start: 0.8163 (m100) cc_final: 0.7632 (m100) REVERT: N 50 THR cc_start: 0.9180 (t) cc_final: 0.8457 (p) REVERT: N 51 ILE cc_start: 0.9253 (tt) cc_final: 0.8866 (tt) outliers start: 3 outliers final: 2 residues processed: 236 average time/residue: 0.2105 time to fit residues: 65.8441 Evaluate side-chains 190 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 58 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7938 Z= 0.253 Angle : 0.730 9.035 10770 Z= 0.386 Chirality : 0.045 0.185 1220 Planarity : 0.005 0.058 1374 Dihedral : 7.434 56.779 1105 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 4.07 % Allowed : 21.89 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.54 (0.22), residues: 989 helix: -3.41 (0.42), residues: 64 sheet: -2.58 (0.31), residues: 249 loop : -3.37 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 300 HIS 0.003 0.001 HIS A 316 PHE 0.016 0.001 PHE N 92 TYR 0.022 0.002 TYR M 87 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 0.905 Fit side-chains REVERT: H 6 GLU cc_start: 0.7958 (mp0) cc_final: 0.7305 (mp0) REVERT: H 12 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7719 (t) REVERT: H 34 MET cc_start: 0.8695 (mmm) cc_final: 0.8212 (mmm) REVERT: H 46 GLU cc_start: 0.6696 (tt0) cc_final: 0.6345 (tt0) REVERT: H 79 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8905 (mmtm) REVERT: H 101 MET cc_start: 0.8657 (mmm) cc_final: 0.8369 (mtm) REVERT: L 37 GLN cc_start: 0.9472 (tm-30) cc_final: 0.8926 (tm-30) REVERT: L 38 GLN cc_start: 0.9156 (pp30) cc_final: 0.8560 (pm20) REVERT: L 42 GLN cc_start: 0.8522 (mp10) cc_final: 0.8238 (mp10) REVERT: L 78 LEU cc_start: 0.8892 (mm) cc_final: 0.8606 (mm) REVERT: L 79 GLU cc_start: 0.8769 (tp30) cc_final: 0.8513 (tp30) REVERT: L 101 ASN cc_start: 0.8875 (p0) cc_final: 0.8303 (p0) REVERT: A 125 PHE cc_start: 0.8521 (m-10) cc_final: 0.8017 (m-10) REVERT: A 147 MET cc_start: 0.7637 (tmm) cc_final: 0.6814 (tmm) REVERT: A 279 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8265 (mmmm) REVERT: A 313 LYS cc_start: 0.9331 (tppp) cc_final: 0.9066 (tppt) REVERT: A 486 GLU cc_start: 0.8971 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 492 MET cc_start: 0.9268 (tmm) cc_final: 0.8888 (tmm) REVERT: A 589 GLN cc_start: 0.8492 (pm20) cc_final: 0.8228 (pm20) REVERT: A 609 HIS cc_start: 0.8189 (m90) cc_final: 0.7717 (m90) REVERT: A 635 ASN cc_start: 0.8977 (p0) cc_final: 0.8710 (m-40) REVERT: A 644 TYR cc_start: 0.8769 (m-10) cc_final: 0.8522 (m-80) REVERT: A 653 ASN cc_start: 0.8859 (t0) cc_final: 0.8260 (t0) REVERT: A 663 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8419 (tm-30) REVERT: M 36 TYR cc_start: 0.6965 (m-80) cc_final: 0.6107 (m-80) REVERT: M 92 PHE cc_start: 0.4148 (OUTLIER) cc_final: 0.3468 (t80) REVERT: M 99 ASN cc_start: 0.8917 (t0) cc_final: 0.8623 (t0) REVERT: N 34 MET cc_start: 0.9197 (mmp) cc_final: 0.8631 (mmp) REVERT: N 36 TRP cc_start: 0.8127 (m100) cc_final: 0.7614 (m100) REVERT: N 50 THR cc_start: 0.9192 (t) cc_final: 0.8320 (p) outliers start: 35 outliers final: 20 residues processed: 215 average time/residue: 0.1848 time to fit residues: 53.9211 Evaluate side-chains 210 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 77 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 71 optimal weight: 0.0770 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN H 100 ASN A 299 HIS A 563 ASN M 6 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7938 Z= 0.242 Angle : 0.707 9.178 10770 Z= 0.369 Chirality : 0.045 0.165 1220 Planarity : 0.004 0.053 1374 Dihedral : 6.970 54.106 1105 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 5.12 % Allowed : 23.86 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.14 (0.23), residues: 989 helix: -2.31 (0.53), residues: 70 sheet: -2.34 (0.32), residues: 242 loop : -3.17 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 300 HIS 0.003 0.001 HIS A 316 PHE 0.021 0.001 PHE A 219 TYR 0.023 0.002 TYR M 87 ARG 0.002 0.000 ARG H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 0.882 Fit side-chains REVERT: H 6 GLU cc_start: 0.7788 (mp0) cc_final: 0.7271 (mp0) REVERT: H 34 MET cc_start: 0.8804 (mmm) cc_final: 0.8273 (mmm) REVERT: H 79 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8919 (mmtm) REVERT: H 101 MET cc_start: 0.8794 (mmm) cc_final: 0.8461 (mtt) REVERT: L 35 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6649 (m-10) REVERT: L 37 GLN cc_start: 0.9461 (tm-30) cc_final: 0.8965 (tm-30) REVERT: L 38 GLN cc_start: 0.9136 (pp30) cc_final: 0.8030 (pp30) REVERT: L 39 LYS cc_start: 0.8896 (tppt) cc_final: 0.8409 (tppt) REVERT: L 78 LEU cc_start: 0.8832 (mm) cc_final: 0.8578 (mm) REVERT: L 79 GLU cc_start: 0.8746 (tp30) cc_final: 0.8505 (tp30) REVERT: A 125 PHE cc_start: 0.8392 (m-10) cc_final: 0.7915 (m-10) REVERT: A 147 MET cc_start: 0.7615 (tmm) cc_final: 0.6765 (tmm) REVERT: A 181 TYR cc_start: 0.7632 (m-80) cc_final: 0.7307 (m-10) REVERT: A 313 LYS cc_start: 0.9329 (tppp) cc_final: 0.9043 (tppt) REVERT: A 343 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (tp) REVERT: A 486 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 492 MET cc_start: 0.9296 (tmm) cc_final: 0.8974 (tmm) REVERT: A 569 GLU cc_start: 0.8861 (pm20) cc_final: 0.8535 (pm20) REVERT: A 589 GLN cc_start: 0.8507 (pm20) cc_final: 0.8235 (pm20) REVERT: A 609 HIS cc_start: 0.8096 (m90) cc_final: 0.7660 (m90) REVERT: A 635 ASN cc_start: 0.8920 (p0) cc_final: 0.8674 (m-40) REVERT: A 644 TYR cc_start: 0.8754 (m-10) cc_final: 0.8526 (m-80) REVERT: A 647 ASP cc_start: 0.8821 (t0) cc_final: 0.8616 (t0) REVERT: A 653 ASN cc_start: 0.8801 (t0) cc_final: 0.8198 (t0) REVERT: A 663 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8365 (tm-30) REVERT: M 36 TYR cc_start: 0.7031 (m-80) cc_final: 0.6173 (m-80) REVERT: M 92 PHE cc_start: 0.3854 (OUTLIER) cc_final: 0.3270 (t80) REVERT: M 99 ASN cc_start: 0.8952 (t0) cc_final: 0.8671 (t0) REVERT: N 32 TYR cc_start: 0.7654 (m-80) cc_final: 0.7374 (m-80) REVERT: N 34 MET cc_start: 0.9116 (mmp) cc_final: 0.8853 (mmp) REVERT: N 36 TRP cc_start: 0.7959 (m100) cc_final: 0.7540 (m100) REVERT: N 71 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6560 (ttm170) REVERT: N 108 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7882 (m-40) outliers start: 44 outliers final: 30 residues processed: 219 average time/residue: 0.1909 time to fit residues: 56.3265 Evaluate side-chains 222 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7938 Z= 0.339 Angle : 0.748 8.931 10770 Z= 0.393 Chirality : 0.046 0.168 1220 Planarity : 0.005 0.053 1374 Dihedral : 7.120 52.854 1105 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.78 % Favored : 83.22 % Rotamer: Outliers : 7.45 % Allowed : 22.93 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.04 (0.23), residues: 989 helix: -1.99 (0.53), residues: 70 sheet: -2.23 (0.34), residues: 234 loop : -3.14 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 300 HIS 0.005 0.001 HIS A 316 PHE 0.025 0.002 PHE A 219 TYR 0.022 0.002 TYR M 87 ARG 0.003 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 192 time to evaluate : 0.956 Fit side-chains REVERT: H 6 GLU cc_start: 0.7945 (mp0) cc_final: 0.7721 (mp0) REVERT: H 34 MET cc_start: 0.8760 (mmm) cc_final: 0.8246 (mmm) REVERT: H 79 LYS cc_start: 0.9238 (mmtp) cc_final: 0.8907 (mmtm) REVERT: H 101 MET cc_start: 0.8808 (mmm) cc_final: 0.8515 (mtt) REVERT: L 35 TRP cc_start: 0.7617 (OUTLIER) cc_final: 0.6591 (m-10) REVERT: L 37 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9163 (tm-30) REVERT: L 38 GLN cc_start: 0.9102 (pp30) cc_final: 0.8036 (pp30) REVERT: L 39 LYS cc_start: 0.8884 (tppt) cc_final: 0.8312 (tppt) REVERT: L 78 LEU cc_start: 0.8799 (mm) cc_final: 0.8558 (mm) REVERT: L 79 GLU cc_start: 0.8726 (tp30) cc_final: 0.8518 (tp30) REVERT: L 101 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8548 (p0) REVERT: A 125 PHE cc_start: 0.8454 (m-10) cc_final: 0.8004 (m-10) REVERT: A 147 MET cc_start: 0.7517 (tmm) cc_final: 0.6657 (tmm) REVERT: A 279 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8206 (mmmm) REVERT: A 313 LYS cc_start: 0.9357 (tppp) cc_final: 0.9077 (tppt) REVERT: A 486 GLU cc_start: 0.8971 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 492 MET cc_start: 0.9288 (tmm) cc_final: 0.8948 (tmm) REVERT: A 609 HIS cc_start: 0.8092 (m90) cc_final: 0.7692 (m90) REVERT: A 635 ASN cc_start: 0.8937 (p0) cc_final: 0.8717 (m-40) REVERT: A 644 TYR cc_start: 0.8797 (m-10) cc_final: 0.8575 (m-80) REVERT: A 653 ASN cc_start: 0.8830 (t0) cc_final: 0.8276 (t0) REVERT: A 663 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8427 (tm-30) REVERT: M 36 TYR cc_start: 0.7024 (m-80) cc_final: 0.6189 (m-80) REVERT: M 92 PHE cc_start: 0.3918 (OUTLIER) cc_final: 0.3394 (t80) REVERT: M 99 ASN cc_start: 0.9011 (t0) cc_final: 0.8766 (t0) REVERT: N 34 MET cc_start: 0.9018 (mmp) cc_final: 0.8780 (mmp) REVERT: N 36 TRP cc_start: 0.7988 (m100) cc_final: 0.7645 (m100) REVERT: N 71 ARG cc_start: 0.7012 (ttm-80) cc_final: 0.6426 (ttm170) REVERT: N 108 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8057 (m-40) outliers start: 64 outliers final: 45 residues processed: 229 average time/residue: 0.2482 time to fit residues: 76.0738 Evaluate side-chains 237 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.0970 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7938 Z= 0.241 Angle : 0.699 8.959 10770 Z= 0.364 Chirality : 0.044 0.163 1220 Planarity : 0.004 0.053 1374 Dihedral : 6.712 50.576 1105 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 6.64 % Allowed : 24.45 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.88 (0.24), residues: 989 helix: -1.46 (0.54), residues: 76 sheet: -2.18 (0.33), residues: 242 loop : -3.07 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 35 HIS 0.003 0.001 HIS A 316 PHE 0.013 0.001 PHE A 219 TYR 0.020 0.001 TYR M 87 ARG 0.002 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 194 time to evaluate : 0.874 Fit side-chains REVERT: H 6 GLU cc_start: 0.8008 (mp0) cc_final: 0.7713 (mp0) REVERT: H 34 MET cc_start: 0.8820 (mmm) cc_final: 0.8253 (mmm) REVERT: H 46 GLU cc_start: 0.6385 (tt0) cc_final: 0.5799 (tt0) REVERT: H 79 LYS cc_start: 0.9224 (mmtp) cc_final: 0.8891 (mmtm) REVERT: H 101 MET cc_start: 0.8815 (mmm) cc_final: 0.8419 (mtt) REVERT: L 35 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: L 37 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9150 (tm-30) REVERT: L 38 GLN cc_start: 0.9031 (pp30) cc_final: 0.8537 (pp30) REVERT: L 39 LYS cc_start: 0.9065 (tppt) cc_final: 0.8856 (tppt) REVERT: L 70 GLU cc_start: 0.8803 (pp20) cc_final: 0.8418 (pp20) REVERT: L 78 LEU cc_start: 0.8777 (mm) cc_final: 0.8551 (mm) REVERT: L 79 GLU cc_start: 0.8674 (tp30) cc_final: 0.8473 (tp30) REVERT: L 101 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8187 (p0) REVERT: A 125 PHE cc_start: 0.8410 (m-10) cc_final: 0.8018 (m-10) REVERT: A 147 MET cc_start: 0.7464 (tmm) cc_final: 0.6611 (tmm) REVERT: A 181 TYR cc_start: 0.7453 (m-80) cc_final: 0.7153 (m-80) REVERT: A 279 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8217 (mmmm) REVERT: A 313 LYS cc_start: 0.9358 (tppp) cc_final: 0.9055 (tppt) REVERT: A 344 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 486 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 492 MET cc_start: 0.9270 (tmm) cc_final: 0.8925 (tmm) REVERT: A 569 GLU cc_start: 0.8922 (pm20) cc_final: 0.8678 (pm20) REVERT: A 609 HIS cc_start: 0.8001 (m90) cc_final: 0.7576 (m90) REVERT: A 644 TYR cc_start: 0.8749 (m-10) cc_final: 0.8539 (m-80) REVERT: A 653 ASN cc_start: 0.8812 (t0) cc_final: 0.8267 (t0) REVERT: A 663 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8388 (tm-30) REVERT: M 36 TYR cc_start: 0.7041 (m-80) cc_final: 0.6220 (m-80) REVERT: M 69 THR cc_start: 0.5805 (OUTLIER) cc_final: 0.5567 (m) REVERT: M 92 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3773 (t80) REVERT: M 99 ASN cc_start: 0.9004 (t0) cc_final: 0.8767 (t0) REVERT: N 34 MET cc_start: 0.8854 (mmp) cc_final: 0.8600 (mmp) REVERT: N 36 TRP cc_start: 0.7712 (m100) cc_final: 0.7424 (m100) REVERT: N 71 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6528 (ttm170) REVERT: N 108 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7997 (m-40) outliers start: 57 outliers final: 42 residues processed: 225 average time/residue: 0.1877 time to fit residues: 57.5070 Evaluate side-chains 235 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 188 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7938 Z= 0.158 Angle : 0.653 8.838 10770 Z= 0.332 Chirality : 0.043 0.163 1220 Planarity : 0.004 0.046 1374 Dihedral : 5.975 47.739 1105 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 5.94 % Allowed : 26.19 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.56 (0.24), residues: 989 helix: -0.71 (0.59), residues: 71 sheet: -1.89 (0.33), residues: 251 loop : -2.94 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 35 HIS 0.001 0.000 HIS A 316 PHE 0.009 0.001 PHE N 92 TYR 0.015 0.001 TYR M 87 ARG 0.003 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 209 time to evaluate : 0.904 Fit side-chains REVERT: H 46 GLU cc_start: 0.6329 (tt0) cc_final: 0.5914 (tt0) REVERT: H 79 LYS cc_start: 0.9178 (mmtp) cc_final: 0.8862 (mmtm) REVERT: H 101 MET cc_start: 0.8720 (mmm) cc_final: 0.8353 (mtt) REVERT: L 35 TRP cc_start: 0.7218 (m-10) cc_final: 0.6631 (m-10) REVERT: L 37 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9118 (tm-30) REVERT: L 38 GLN cc_start: 0.8997 (pp30) cc_final: 0.8524 (pp30) REVERT: L 39 LYS cc_start: 0.9018 (tppt) cc_final: 0.8637 (tppt) REVERT: L 79 GLU cc_start: 0.8593 (tp30) cc_final: 0.8342 (tp30) REVERT: L 101 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8469 (p0) REVERT: A 83 MET cc_start: 0.8413 (tpp) cc_final: 0.8132 (mmm) REVERT: A 115 ASP cc_start: 0.3497 (OUTLIER) cc_final: 0.3272 (m-30) REVERT: A 125 PHE cc_start: 0.8421 (m-10) cc_final: 0.7994 (m-10) REVERT: A 147 MET cc_start: 0.7511 (tmm) cc_final: 0.6693 (tmm) REVERT: A 181 TYR cc_start: 0.7390 (m-80) cc_final: 0.7126 (m-10) REVERT: A 252 HIS cc_start: 0.8042 (m-70) cc_final: 0.7338 (m-70) REVERT: A 313 LYS cc_start: 0.9312 (tppp) cc_final: 0.9101 (ttpp) REVERT: A 344 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 486 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 492 MET cc_start: 0.9266 (tmm) cc_final: 0.8980 (tmm) REVERT: A 569 GLU cc_start: 0.8933 (pm20) cc_final: 0.8691 (pm20) REVERT: A 593 GLN cc_start: 0.9070 (pm20) cc_final: 0.8846 (pm20) REVERT: A 609 HIS cc_start: 0.8108 (m90) cc_final: 0.7696 (m90) REVERT: A 653 ASN cc_start: 0.8773 (t0) cc_final: 0.8204 (t0) REVERT: A 663 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8401 (tm-30) REVERT: M 36 TYR cc_start: 0.7054 (m-80) cc_final: 0.6277 (m-80) REVERT: M 69 THR cc_start: 0.5829 (OUTLIER) cc_final: 0.5563 (m) REVERT: M 77 ASP cc_start: 0.8459 (m-30) cc_final: 0.8150 (m-30) REVERT: N 27 PHE cc_start: 0.7203 (p90) cc_final: 0.6894 (p90) REVERT: N 71 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6694 (ttm170) REVERT: N 108 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (m-40) outliers start: 51 outliers final: 35 residues processed: 238 average time/residue: 0.1908 time to fit residues: 61.2178 Evaluate side-chains 227 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.0980 chunk 54 optimal weight: 0.0060 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.0040 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7938 Z= 0.155 Angle : 0.670 9.149 10770 Z= 0.336 Chirality : 0.043 0.163 1220 Planarity : 0.004 0.046 1374 Dihedral : 5.459 47.128 1103 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 5.24 % Allowed : 28.52 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.24), residues: 989 helix: -0.22 (0.63), residues: 71 sheet: -1.72 (0.33), residues: 253 loop : -2.85 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 36 HIS 0.001 0.000 HIS A 610 PHE 0.006 0.001 PHE M 62 TYR 0.014 0.001 TYR M 87 ARG 0.005 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8876 (mmm) cc_final: 0.8564 (mmm) REVERT: H 46 GLU cc_start: 0.6477 (tt0) cc_final: 0.6090 (tt0) REVERT: H 79 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8850 (mmtm) REVERT: H 93 CYS cc_start: 0.8103 (m) cc_final: 0.7693 (t) REVERT: H 101 MET cc_start: 0.8705 (mmm) cc_final: 0.8376 (mtt) REVERT: L 35 TRP cc_start: 0.7055 (m-10) cc_final: 0.6640 (m-10) REVERT: L 37 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8857 (tm-30) REVERT: L 38 GLN cc_start: 0.8952 (pp30) cc_final: 0.8552 (pp30) REVERT: L 39 LYS cc_start: 0.8998 (tppt) cc_final: 0.8776 (tppt) REVERT: L 48 ILE cc_start: 0.9503 (mm) cc_final: 0.9291 (mm) REVERT: A 83 MET cc_start: 0.8275 (tpp) cc_final: 0.8015 (mmm) REVERT: A 115 ASP cc_start: 0.3687 (OUTLIER) cc_final: 0.3436 (m-30) REVERT: A 147 MET cc_start: 0.7570 (tmm) cc_final: 0.6703 (tmm) REVERT: A 486 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 492 MET cc_start: 0.9237 (tmm) cc_final: 0.8925 (tmm) REVERT: A 569 GLU cc_start: 0.8918 (pm20) cc_final: 0.8714 (pm20) REVERT: A 589 GLN cc_start: 0.8471 (pm20) cc_final: 0.8261 (pm20) REVERT: A 593 GLN cc_start: 0.9044 (pm20) cc_final: 0.8844 (pm20) REVERT: A 609 HIS cc_start: 0.8093 (m90) cc_final: 0.7707 (m90) REVERT: A 663 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8426 (tm-30) REVERT: M 36 TYR cc_start: 0.7046 (m-80) cc_final: 0.6312 (m-80) REVERT: M 42 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7467 (tp-100) REVERT: M 69 THR cc_start: 0.5540 (OUTLIER) cc_final: 0.5253 (m) REVERT: M 77 ASP cc_start: 0.8488 (m-30) cc_final: 0.8184 (m-30) REVERT: N 36 TRP cc_start: 0.7636 (m100) cc_final: 0.7210 (m100) REVERT: N 71 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6934 (ttm170) REVERT: N 108 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7361 (m-40) outliers start: 45 outliers final: 30 residues processed: 226 average time/residue: 0.1786 time to fit residues: 55.2590 Evaluate side-chains 226 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 59 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7938 Z= 0.327 Angle : 0.755 9.282 10770 Z= 0.389 Chirality : 0.046 0.160 1220 Planarity : 0.005 0.072 1374 Dihedral : 6.228 49.432 1103 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 6.05 % Allowed : 27.94 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.46 (0.25), residues: 989 helix: -0.55 (0.64), residues: 63 sheet: -1.94 (0.32), residues: 269 loop : -2.80 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 35 HIS 0.005 0.001 HIS A 316 PHE 0.019 0.002 PHE A 219 TYR 0.018 0.002 TYR M 87 ARG 0.004 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 2 GLN cc_start: 0.9443 (OUTLIER) cc_final: 0.9061 (pm20) REVERT: H 46 GLU cc_start: 0.6485 (tt0) cc_final: 0.6101 (tt0) REVERT: H 101 MET cc_start: 0.8770 (mmm) cc_final: 0.8405 (mtt) REVERT: L 35 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: L 37 GLN cc_start: 0.9396 (tm-30) cc_final: 0.9138 (tm-30) REVERT: L 38 GLN cc_start: 0.9084 (pp30) cc_final: 0.8555 (pp30) REVERT: L 39 LYS cc_start: 0.9131 (tppt) cc_final: 0.8773 (tppt) REVERT: L 70 GLU cc_start: 0.8825 (pp20) cc_final: 0.8416 (pp20) REVERT: A 147 MET cc_start: 0.7520 (tmm) cc_final: 0.6916 (tmm) REVERT: A 181 TYR cc_start: 0.7255 (m-80) cc_final: 0.6992 (m-80) REVERT: A 492 MET cc_start: 0.9273 (tmm) cc_final: 0.8974 (tmm) REVERT: A 569 GLU cc_start: 0.8947 (pm20) cc_final: 0.8707 (pm20) REVERT: A 582 LYS cc_start: 0.8871 (tptt) cc_final: 0.8156 (tptp) REVERT: A 593 GLN cc_start: 0.9171 (pm20) cc_final: 0.8956 (pm20) REVERT: A 609 HIS cc_start: 0.8151 (m90) cc_final: 0.7770 (m90) REVERT: A 653 ASN cc_start: 0.8769 (t0) cc_final: 0.8333 (t0) REVERT: A 663 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8451 (tm-30) REVERT: M 69 THR cc_start: 0.5861 (OUTLIER) cc_final: 0.5583 (m) REVERT: M 77 ASP cc_start: 0.8422 (m-30) cc_final: 0.8138 (m-30) REVERT: N 27 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7005 (p90) REVERT: N 36 TRP cc_start: 0.8015 (m100) cc_final: 0.7708 (m100) REVERT: N 71 ARG cc_start: 0.6929 (ttm-80) cc_final: 0.6517 (ttm170) REVERT: N 108 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7813 (m-40) outliers start: 52 outliers final: 40 residues processed: 223 average time/residue: 0.1814 time to fit residues: 55.4437 Evaluate side-chains 233 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 382 TRP Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7938 Z= 0.181 Angle : 0.707 10.391 10770 Z= 0.353 Chirality : 0.044 0.162 1220 Planarity : 0.004 0.074 1374 Dihedral : 5.699 48.796 1103 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 5.01 % Allowed : 29.10 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.32 (0.25), residues: 989 helix: -0.07 (0.63), residues: 70 sheet: -1.87 (0.32), residues: 258 loop : -2.76 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 35 HIS 0.002 0.000 HIS A 316 PHE 0.008 0.001 PHE L 62 TYR 0.016 0.001 TYR M 87 ARG 0.005 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 0.966 Fit side-chains REVERT: H 2 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9228 (pm20) REVERT: H 34 MET cc_start: 0.8838 (mmm) cc_final: 0.8216 (mmm) REVERT: H 46 GLU cc_start: 0.6465 (tt0) cc_final: 0.6248 (tt0) REVERT: H 79 LYS cc_start: 0.9169 (mmtp) cc_final: 0.8823 (mmtm) REVERT: H 101 MET cc_start: 0.8696 (mmm) cc_final: 0.8322 (mtt) REVERT: L 37 GLN cc_start: 0.9352 (tm-30) cc_final: 0.8859 (tm-30) REVERT: L 38 GLN cc_start: 0.9005 (pp30) cc_final: 0.8466 (pp30) REVERT: L 39 LYS cc_start: 0.9110 (tppt) cc_final: 0.8760 (tppt) REVERT: L 70 GLU cc_start: 0.8815 (pp20) cc_final: 0.8376 (pp20) REVERT: L 79 GLU cc_start: 0.8375 (tp30) cc_final: 0.7976 (tp30) REVERT: A 83 MET cc_start: 0.8461 (tpp) cc_final: 0.8222 (mmm) REVERT: A 147 MET cc_start: 0.7520 (tmm) cc_final: 0.6695 (tmm) REVERT: A 344 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7392 (mp0) REVERT: A 486 GLU cc_start: 0.8896 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 492 MET cc_start: 0.9318 (tmm) cc_final: 0.9028 (tmm) REVERT: A 569 GLU cc_start: 0.8903 (pm20) cc_final: 0.8689 (pm20) REVERT: A 593 GLN cc_start: 0.9111 (pm20) cc_final: 0.8897 (pm20) REVERT: A 609 HIS cc_start: 0.8051 (m90) cc_final: 0.7695 (m90) REVERT: A 653 ASN cc_start: 0.8753 (t0) cc_final: 0.8304 (t0) REVERT: A 663 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8464 (tm-30) REVERT: M 36 TYR cc_start: 0.7142 (m-80) cc_final: 0.6386 (m-80) REVERT: M 42 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7548 (tp-100) REVERT: M 69 THR cc_start: 0.5600 (OUTLIER) cc_final: 0.5316 (m) REVERT: M 77 ASP cc_start: 0.8398 (m-30) cc_final: 0.8084 (m-30) REVERT: N 27 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6939 (p90) REVERT: N 36 TRP cc_start: 0.7955 (m100) cc_final: 0.7588 (m100) REVERT: N 71 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6711 (ttm170) REVERT: N 108 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7237 (m-40) outliers start: 43 outliers final: 35 residues processed: 216 average time/residue: 0.1976 time to fit residues: 59.4360 Evaluate side-chains 228 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 108 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7938 Z= 0.209 Angle : 0.713 9.924 10770 Z= 0.358 Chirality : 0.045 0.161 1220 Planarity : 0.004 0.070 1374 Dihedral : 5.725 49.445 1103 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 4.66 % Allowed : 29.10 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.31 (0.25), residues: 989 helix: 0.02 (0.64), residues: 69 sheet: -1.89 (0.32), residues: 261 loop : -2.75 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 110 HIS 0.003 0.000 HIS A 316 PHE 0.013 0.001 PHE A 219 TYR 0.017 0.001 TYR M 87 ARG 0.005 0.000 ARG L 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.8882 (mmm) cc_final: 0.8295 (mmm) REVERT: H 46 GLU cc_start: 0.6484 (tt0) cc_final: 0.6247 (tt0) REVERT: H 101 MET cc_start: 0.8722 (mmm) cc_final: 0.8372 (mtt) REVERT: L 37 GLN cc_start: 0.9364 (tm-30) cc_final: 0.8883 (tm-30) REVERT: L 38 GLN cc_start: 0.9024 (pp30) cc_final: 0.8488 (pp30) REVERT: L 39 LYS cc_start: 0.9167 (tppt) cc_final: 0.8819 (tppt) REVERT: L 70 GLU cc_start: 0.8816 (pp20) cc_final: 0.8374 (pp20) REVERT: L 79 GLU cc_start: 0.8357 (tp30) cc_final: 0.7945 (tp30) REVERT: A 83 MET cc_start: 0.8433 (tpp) cc_final: 0.8201 (mmm) REVERT: A 147 MET cc_start: 0.7537 (tmm) cc_final: 0.6700 (tmm) REVERT: A 181 TYR cc_start: 0.7103 (m-80) cc_final: 0.6841 (m-10) REVERT: A 212 MET cc_start: 0.8045 (mtt) cc_final: 0.7825 (mtt) REVERT: A 344 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7414 (mp0) REVERT: A 486 GLU cc_start: 0.8899 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 492 MET cc_start: 0.9301 (tmm) cc_final: 0.9009 (tmm) REVERT: A 569 GLU cc_start: 0.8912 (pm20) cc_final: 0.8702 (pm20) REVERT: A 593 GLN cc_start: 0.9095 (pm20) cc_final: 0.8878 (pm20) REVERT: A 609 HIS cc_start: 0.8155 (m90) cc_final: 0.7806 (m90) REVERT: A 653 ASN cc_start: 0.8765 (t0) cc_final: 0.8318 (t0) REVERT: A 663 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8467 (tm-30) REVERT: M 42 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7663 (tp-100) REVERT: M 69 THR cc_start: 0.5652 (OUTLIER) cc_final: 0.5365 (m) REVERT: M 77 ASP cc_start: 0.8399 (m-30) cc_final: 0.8084 (m-30) REVERT: N 27 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6901 (p90) REVERT: N 36 TRP cc_start: 0.8036 (m100) cc_final: 0.7753 (m100) REVERT: N 71 ARG cc_start: 0.6879 (ttm-80) cc_final: 0.6649 (ttm170) REVERT: N 95 ARG cc_start: 0.7632 (tmm-80) cc_final: 0.7250 (tmm-80) outliers start: 40 outliers final: 35 residues processed: 216 average time/residue: 0.1761 time to fit residues: 52.3194 Evaluate side-chains 225 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 484 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 98 TYR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 27 PHE Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN A 77 HIS A 533 GLN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.144476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095677 restraints weight = 16901.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098772 restraints weight = 9195.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100810 restraints weight = 6309.170| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 7938 Z= 0.444 Angle : 0.849 9.848 10770 Z= 0.436 Chirality : 0.049 0.207 1220 Planarity : 0.005 0.065 1374 Dihedral : 6.784 49.934 1103 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.09 % Favored : 82.81 % Rotamer: Outliers : 5.70 % Allowed : 29.10 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.71 (0.24), residues: 989 helix: -1.04 (0.60), residues: 69 sheet: -2.03 (0.33), residues: 253 loop : -2.99 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 300 HIS 0.008 0.001 HIS A 610 PHE 0.022 0.002 PHE A 219 TYR 0.023 0.002 TYR M 87 ARG 0.005 0.001 ARG L 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.28 seconds wall clock time: 36 minutes 9.82 seconds (2169.82 seconds total)