Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 15:24:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/04_2023/7fbi_31515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/04_2023/7fbi_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_31515/04_2023/7fbi_31515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/04_2023/7fbi_31515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/04_2023/7fbi_31515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fbi_31515/04_2023/7fbi_31515.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.51, per 1000 atoms: 0.58 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: 3.10 Conformation dependent library (CDL) restraints added in 1.2 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: 0.48 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: 2.06 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 1.170 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: 6.710 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.900 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.640 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.982 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 236 average time/residue: 0.2129 time to fit residues: 65.8826 Evaluate side-chains 181 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0864 time to fit residues: 1.5371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN A 455 ASN A 487 GLN ** 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: 0.7845 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7938 Z= 0.305 Angle : 0.777 9.199 10770 Z= 0.411 Chirality : 0.046 0.186 1220 Planarity : 0.005 0.058 1374 Dihedral : 7.214 58.053 1099 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -4.60 (0.22), residues: 989 helix: -3.36 (0.42), residues: 64 sheet: -2.64 (0.31), residues: 250 loop : -3.42 (0.19), residues: 675 *********************** 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 238 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 23 residues processed: 212 average time/residue: 0.2044 time to fit residues: 57.4544 Evaluate side-chains 203 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0995 time to fit residues: 4.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 2 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 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: 0.7835 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7938 Z= 0.272 Angle : 0.728 8.868 10770 Z= 0.382 Chirality : 0.046 0.176 1220 Planarity : 0.005 0.058 1374 Dihedral : 6.809 57.120 1099 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.56 % Favored : 85.44 % Rotamer Outliers : 3.14 % 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: -4.27 (0.23), residues: 989 helix: -2.11 (0.53), residues: 70 sheet: -2.48 (0.32), residues: 245 loop : -3.27 (0.20), residues: 674 *********************** 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 222 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 213 average time/residue: 0.1833 time to fit residues: 52.9121 Evaluate side-chains 187 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0665 time to fit residues: 2.5591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 A 299 HIS ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7938 Z= 0.183 Angle : 0.681 8.328 10770 Z= 0.352 Chirality : 0.044 0.175 1220 Planarity : 0.004 0.051 1374 Dihedral : 6.226 51.283 1099 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer Outliers : 3.38 % 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: -1.17 (0.59), residues: 70 sheet: -2.15 (0.32), residues: 255 loop : -3.11 (0.20), residues: 664 *********************** 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 226 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 210 average time/residue: 0.1920 time to fit residues: 54.9178 Evaluate side-chains 205 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0757 time to fit residues: 3.5937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 563 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: 0.7836 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 7938 Z= 0.303 Angle : 0.742 10.962 10770 Z= 0.384 Chirality : 0.045 0.172 1220 Planarity : 0.005 0.050 1374 Dihedral : 6.422 47.157 1099 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer Outliers : 2.68 % 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: -3.91 (0.24), residues: 989 helix: -1.36 (0.58), residues: 70 sheet: -2.21 (0.32), residues: 251 loop : -3.09 (0.21), residues: 668 *********************** 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 216 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 0.988 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 209 average time/residue: 0.1916 time to fit residues: 54.5374 Evaluate side-chains 199 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0704 time to fit residues: 2.9445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 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** A 455 ASN ** A 563 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3455 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= 0.202 Angle : 0.696 9.811 10770 Z= 0.354 Chirality : 0.044 0.168 1220 Planarity : 0.004 0.047 1374 Dihedral : 5.968 36.559 1099 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer Outliers : 3.73 % 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: -3.70 (0.24), residues: 989 helix: -0.73 (0.59), residues: 75 sheet: -2.10 (0.32), residues: 261 loop : -3.01 (0.21), residues: 653 *********************** 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 231 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 215 average time/residue: 0.1880 time to fit residues: 55.0152 Evaluate side-chains 201 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0871 time to fit residues: 3.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7938 Z= 0.173 Angle : 0.698 9.286 10770 Z= 0.352 Chirality : 0.044 0.165 1220 Planarity : 0.004 0.042 1374 Dihedral : 5.624 33.296 1099 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer Outliers : 2.68 % 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: -3.52 (0.24), residues: 989 helix: -0.20 (0.63), residues: 69 sheet: -1.94 (0.32), residues: 259 loop : -2.94 (0.21), residues: 661 *********************** 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 226 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.000 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 216 average time/residue: 0.1794 time to fit residues: 53.1099 Evaluate side-chains 208 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0745 time to fit residues: 3.1762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 533 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7938 Z= 0.217 Angle : 0.732 9.449 10770 Z= 0.369 Chirality : 0.046 0.168 1220 Planarity : 0.005 0.079 1374 Dihedral : 5.719 33.675 1099 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer Outliers : 2.21 % 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: -3.48 (0.25), residues: 989 helix: -0.11 (0.64), residues: 69 sheet: -1.92 (0.33), residues: 253 loop : -2.90 (0.21), residues: 667 *********************** 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 220 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.949 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 207 average time/residue: 0.1953 time to fit residues: 54.9260 Evaluate side-chains 207 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0761 time to fit residues: 3.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 40.0000 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7938 Z= 0.251 Angle : 0.757 13.033 10770 Z= 0.380 Chirality : 0.046 0.164 1220 Planarity : 0.005 0.063 1374 Dihedral : 5.870 34.716 1099 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer Outliers : 1.05 % 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: -3.51 (0.25), residues: 989 helix: -0.16 (0.63), residues: 69 sheet: -1.92 (0.33), residues: 247 loop : -2.94 (0.21), residues: 673 *********************** 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 202 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.976 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 198 average time/residue: 0.1909 time to fit residues: 51.5710 Evaluate side-chains 191 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0694 time to fit residues: 1.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN N 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7938 Z= 0.294 Angle : 0.809 14.393 10770 Z= 0.404 Chirality : 0.047 0.184 1220 Planarity : 0.005 0.058 1374 Dihedral : 6.031 33.574 1099 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer Outliers : 1.28 % 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: -3.60 (0.24), residues: 989 helix: -0.55 (0.60), residues: 75 sheet: -2.00 (0.32), residues: 255 loop : -2.97 (0.21), residues: 659 ********************** 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 201 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 0.909 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 194 average time/residue: 0.1869 time to fit residues: 49.7372 Evaluate side-chains 198 residues out of total 859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0841 time to fit residues: 2.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099344 restraints weight = 16959.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102608 restraints weight = 9069.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104750 restraints weight = 6146.703| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 7938 Z= 0.300 Angle : 0.797 13.741 10770 Z= 0.401 Chirality : 0.046 0.168 1220 Planarity : 0.005 0.054 1374 Dihedral : 6.139 34.123 1099 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer Outliers : 0.47 % 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: -3.69 (0.24), residues: 989 helix: -0.65 (0.59), residues: 75 sheet: -2.08 (0.32), residues: 245 loop : -3.01 (0.21), residues: 669 =============================================================================== Job complete usr+sys time: 1829.77 seconds wall clock time: 33 minutes 51.40 seconds (2031.40 seconds total)