Starting phenix.real_space_refine on Mon Mar 11 00:18:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/03_2024/6vrk_21369_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 124": "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: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.09, per 1000 atoms: 0.67 Number of scatterers: 6141 At special positions: 0 Unit cell: (97.2, 102.384, 82.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 6 sheets defined 49.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.566A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 4.976A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.672A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.539A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.637A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.056A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 4.056A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.743A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 389 removed outlier: 3.653A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 404 through 407 No H-bonds generated for 'chain 'A' and resid 404 through 407' Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 420 through 453 removed outlier: 4.170A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.461A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 556 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.044A pdb=" N THR A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing sheet with id= A, first strand: chain 'C' and resid 24 through 26 Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 Processing sheet with id= C, first strand: chain 'C' and resid 105 through 110 removed outlier: 3.635A pdb=" N VAL C 105 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 58 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 107 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.646A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.989A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 112 through 118 removed outlier: 3.610A pdb=" N TYR B 114 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 56 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 118 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 55 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 630 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: 1.71 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 1822 1.36 - 1.49: 1931 1.49 - 1.63: 2523 1.63 - 1.76: 0 1.76 - 1.89: 50 Bond restraints: 6326 Sorted by residual: bond pdb=" C14 RFS A 704 " pdb=" O15 RFS A 704 " ideal model delta sigma weight residual 1.401 1.499 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C06 RFS A 704 " pdb=" C07 RFS A 704 " ideal model delta sigma weight residual 1.514 1.602 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C07 RFS A 704 " pdb=" C08 RFS A 704 " ideal model delta sigma weight residual 1.386 1.456 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C08 RFS A 704 " pdb=" C09 RFS A 704 " ideal model delta sigma weight residual 1.386 1.332 0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" C16 RFS A 704 " pdb=" C17 RFS A 704 " ideal model delta sigma weight residual 1.387 1.439 -0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.03: 188 107.03 - 113.78: 3469 113.78 - 120.54: 2513 120.54 - 127.29: 2366 127.29 - 134.04: 83 Bond angle restraints: 8619 Sorted by residual: angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 133.41 -11.61 2.44e+00 1.68e-01 2.26e+01 angle pdb=" N ILE A 587 " pdb=" CA ILE A 587 " pdb=" C ILE A 587 " ideal model delta sigma weight residual 112.98 107.67 5.31 1.25e+00 6.40e-01 1.81e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.87 -8.06 2.21e+00 2.05e-01 1.33e+01 angle pdb=" C01 RFS A 704 " pdb=" C06 RFS A 704 " pdb=" C05 RFS A 704 " ideal model delta sigma weight residual 107.16 116.54 -9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" C2 LMT A 703 " pdb=" C3 LMT A 703 " pdb=" C4 LMT A 703 " ideal model delta sigma weight residual 117.09 107.89 9.20 3.00e+00 1.11e-01 9.40e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 3526 26.63 - 53.27: 133 53.27 - 79.90: 12 79.90 - 106.53: 3 106.53 - 133.17: 2 Dihedral angle restraints: 3676 sinusoidal: 1462 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 135.50 44.50 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 108 " pdb=" CB CYS C 108 " ideal model delta sinusoidal sigma weight residual -86.00 -33.27 -52.73 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" C04 RFS A 704 " pdb=" C05 RFS A 704 " pdb=" C14 RFS A 704 " pdb=" O15 RFS A 704 " ideal model delta sinusoidal sigma weight residual 13.76 -119.41 133.17 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 3673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 723 0.042 - 0.083: 197 0.083 - 0.125: 41 0.125 - 0.167: 2 0.167 - 0.208: 3 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 703 " pdb=" C4' LMT A 703 " pdb=" C6' LMT A 703 " pdb=" O5' LMT A 703 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3B LMT A 703 " pdb=" C2B LMT A 703 " pdb=" C4B LMT A 703 " pdb=" O3B LMT A 703 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C4' LMT A 703 " pdb=" C3' LMT A 703 " pdb=" C5' LMT A 703 " pdb=" O1B LMT A 703 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 122 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 548 " 0.012 2.00e-02 2.50e+03 9.45e-03 1.56e+00 pdb=" CG PHE A 548 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 548 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 131 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1375 2.78 - 3.31: 6197 3.31 - 3.84: 10512 3.84 - 4.37: 11878 4.37 - 4.90: 20077 Nonbonded interactions: 50039 Sorted by model distance: nonbonded pdb=" O ARG A 596 " pdb=" OG1 THR A 600 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR C 51 " pdb=" O SER C 70 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 385 " pdb=" OD1 ASN A 416 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR A 210 " pdb=" OG SER A 224 " model vdw 2.268 2.440 ... (remaining 50034 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 13.920 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.950 Find NCS groups from input model: 0.150 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.004 0.098 6326 Z= 0.249 Angle : 0.666 11.612 8619 Z= 0.345 Chirality : 0.040 0.208 966 Planarity : 0.004 0.065 1048 Dihedral : 14.197 133.167 2261 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.27), residues: 758 helix: -1.01 (0.23), residues: 359 sheet: -3.09 (0.42), residues: 89 loop : -2.93 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.005 0.001 HIS C 111 PHE 0.021 0.001 PHE A 548 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7388 (tptp) REVERT: A 135 MET cc_start: 0.9118 (tmm) cc_final: 0.8871 (tmm) REVERT: A 152 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6490 (ttm-80) REVERT: A 229 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8683 (tm-30) REVERT: A 417 MET cc_start: 0.6445 (mtm) cc_final: 0.5830 (mtm) REVERT: A 432 ILE cc_start: 0.8960 (mt) cc_final: 0.8707 (mt) REVERT: A 493 GLU cc_start: 0.6717 (tt0) cc_final: 0.6314 (tt0) REVERT: A 494 GLU cc_start: 0.8033 (tp30) cc_final: 0.7783 (tt0) REVERT: A 563 LEU cc_start: 0.8343 (pt) cc_final: 0.6023 (tt) REVERT: C 48 ASP cc_start: 0.7048 (t0) cc_final: 0.6770 (t0) REVERT: C 99 GLN cc_start: 0.6118 (mt0) cc_final: 0.5802 (mt0) REVERT: B 58 GLN cc_start: 0.6535 (tm-30) cc_final: 0.6331 (tm-30) REVERT: B 109 ASP cc_start: 0.7275 (m-30) cc_final: 0.6728 (m-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1830 time to fit residues: 51.4196 Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 240 HIS A 368 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.173 Angle : 0.605 13.803 8619 Z= 0.305 Chirality : 0.039 0.155 966 Planarity : 0.005 0.073 1048 Dihedral : 7.417 121.453 945 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.46 % Allowed : 5.54 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.29), residues: 758 helix: -0.07 (0.26), residues: 356 sheet: -2.77 (0.44), residues: 92 loop : -2.63 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 541 HIS 0.003 0.001 HIS A 143 PHE 0.027 0.001 PHE A 536 TYR 0.016 0.001 TYR B 124 ARG 0.004 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 182 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7260 (tptp) REVERT: A 229 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 238 GLN cc_start: 0.6353 (tp40) cc_final: 0.5444 (tp-100) REVERT: A 410 TYR cc_start: 0.8556 (t80) cc_final: 0.8152 (t80) REVERT: A 417 MET cc_start: 0.6409 (mtm) cc_final: 0.6021 (mtm) REVERT: A 493 GLU cc_start: 0.6330 (tt0) cc_final: 0.6070 (mt-10) REVERT: A 494 GLU cc_start: 0.8089 (tp30) cc_final: 0.7753 (tt0) REVERT: A 563 LEU cc_start: 0.8501 (pt) cc_final: 0.5764 (tt) REVERT: B 108 GLU cc_start: 0.7982 (pp20) cc_final: 0.7716 (pp20) REVERT: B 109 ASP cc_start: 0.7255 (m-30) cc_final: 0.6901 (m-30) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.1594 time to fit residues: 39.1209 Evaluate side-chains 152 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 240 HIS A 391 ASN A 569 ASN C 28 HIS B 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6326 Z= 0.175 Angle : 0.611 14.808 8619 Z= 0.304 Chirality : 0.040 0.161 966 Planarity : 0.004 0.070 1048 Dihedral : 6.883 112.691 945 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.30), residues: 758 helix: 0.24 (0.28), residues: 356 sheet: -2.53 (0.47), residues: 90 loop : -2.40 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 541 HIS 0.003 0.001 HIS C 111 PHE 0.038 0.002 PHE A 373 TYR 0.021 0.001 TYR B 114 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7191 (tptp) REVERT: A 88 PHE cc_start: 0.8257 (t80) cc_final: 0.7995 (t80) REVERT: A 152 ARG cc_start: 0.7065 (ttp-110) cc_final: 0.6149 (ttm-80) REVERT: A 180 MET cc_start: 0.9116 (mmp) cc_final: 0.8827 (mmp) REVERT: A 229 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 310 LEU cc_start: 0.7316 (mp) cc_final: 0.7101 (tp) REVERT: A 493 GLU cc_start: 0.6328 (tt0) cc_final: 0.6079 (mt-10) REVERT: A 563 LEU cc_start: 0.8459 (pt) cc_final: 0.7418 (tt) REVERT: B 108 GLU cc_start: 0.7956 (pp20) cc_final: 0.7743 (pp20) REVERT: B 109 ASP cc_start: 0.7369 (m-30) cc_final: 0.6914 (m-30) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1790 time to fit residues: 41.1244 Evaluate side-chains 149 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6326 Z= 0.148 Angle : 0.585 11.984 8619 Z= 0.292 Chirality : 0.039 0.175 966 Planarity : 0.004 0.071 1048 Dihedral : 6.563 97.499 945 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.30), residues: 758 helix: 0.40 (0.28), residues: 360 sheet: -2.47 (0.46), residues: 97 loop : -2.20 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 458 HIS 0.003 0.001 HIS C 111 PHE 0.036 0.001 PHE C 118 TYR 0.021 0.001 TYR B 114 ARG 0.001 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.738 Fit side-chains REVERT: A 85 LYS cc_start: 0.7528 (tmtt) cc_final: 0.7194 (tptp) REVERT: A 88 PHE cc_start: 0.8346 (t80) cc_final: 0.8057 (t80) REVERT: A 103 TRP cc_start: 0.8029 (p-90) cc_final: 0.7431 (p-90) REVERT: A 152 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6201 (ttm-80) REVERT: A 180 MET cc_start: 0.9130 (mmp) cc_final: 0.8843 (mmp) REVERT: A 229 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 410 TYR cc_start: 0.8529 (t80) cc_final: 0.8130 (t80) REVERT: A 493 GLU cc_start: 0.6282 (tt0) cc_final: 0.6027 (mt-10) REVERT: A 563 LEU cc_start: 0.8446 (pt) cc_final: 0.7474 (tt) REVERT: B 133 THR cc_start: 0.7786 (p) cc_final: 0.7519 (p) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1972 time to fit residues: 44.7498 Evaluate side-chains 139 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6326 Z= 0.273 Angle : 0.703 12.937 8619 Z= 0.356 Chirality : 0.043 0.169 966 Planarity : 0.005 0.073 1048 Dihedral : 7.141 86.671 945 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 758 helix: 0.13 (0.27), residues: 364 sheet: -2.51 (0.47), residues: 96 loop : -2.22 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 271 HIS 0.006 0.002 HIS C 111 PHE 0.023 0.002 PHE C 118 TYR 0.025 0.002 TYR B 114 ARG 0.004 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7354 (tptp) REVERT: A 126 ILE cc_start: 0.8036 (mt) cc_final: 0.7634 (pt) REVERT: A 152 ARG cc_start: 0.7312 (ttp-110) cc_final: 0.6196 (ttm-80) REVERT: A 229 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 563 LEU cc_start: 0.8648 (pt) cc_final: 0.7755 (tt) REVERT: B 133 THR cc_start: 0.7834 (p) cc_final: 0.7568 (p) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1719 time to fit residues: 40.2344 Evaluate side-chains 143 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6326 Z= 0.229 Angle : 0.663 11.224 8619 Z= 0.340 Chirality : 0.042 0.179 966 Planarity : 0.005 0.072 1048 Dihedral : 6.855 74.756 945 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.30), residues: 758 helix: 0.18 (0.27), residues: 357 sheet: -2.57 (0.46), residues: 96 loop : -2.21 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 458 HIS 0.006 0.002 HIS C 111 PHE 0.031 0.002 PHE A 427 TYR 0.023 0.002 TYR B 123 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7566 (tmtt) cc_final: 0.7301 (tptp) REVERT: A 229 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 260 MET cc_start: 0.7683 (ptp) cc_final: 0.7386 (ptm) REVERT: A 563 LEU cc_start: 0.8666 (pt) cc_final: 0.7794 (tt) REVERT: B 108 GLU cc_start: 0.7839 (pp20) cc_final: 0.7609 (pp20) REVERT: B 133 THR cc_start: 0.7832 (p) cc_final: 0.7600 (p) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1655 time to fit residues: 39.2145 Evaluate side-chains 151 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.168 Angle : 0.624 10.165 8619 Z= 0.316 Chirality : 0.040 0.159 966 Planarity : 0.004 0.071 1048 Dihedral : 6.497 68.629 945 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.31), residues: 758 helix: 0.42 (0.27), residues: 351 sheet: -2.42 (0.46), residues: 97 loop : -1.95 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 55 HIS 0.012 0.002 HIS A 240 PHE 0.027 0.002 PHE A 287 TYR 0.018 0.001 TYR B 114 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7174 (tptp) REVERT: A 180 MET cc_start: 0.8713 (mmt) cc_final: 0.7846 (mmt) REVERT: A 229 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8453 (tm-30) REVERT: A 242 SER cc_start: 0.8521 (p) cc_final: 0.8242 (t) REVERT: A 432 ILE cc_start: 0.8878 (mt) cc_final: 0.8493 (mt) REVERT: A 563 LEU cc_start: 0.8596 (pt) cc_final: 0.7704 (tt) REVERT: B 133 THR cc_start: 0.7864 (p) cc_final: 0.7642 (p) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1660 time to fit residues: 39.2982 Evaluate side-chains 142 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.167 Angle : 0.620 10.382 8619 Z= 0.309 Chirality : 0.040 0.160 966 Planarity : 0.004 0.071 1048 Dihedral : 6.101 58.364 945 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.31), residues: 758 helix: 0.38 (0.27), residues: 363 sheet: -2.35 (0.47), residues: 97 loop : -1.84 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.006 0.001 HIS C 111 PHE 0.024 0.001 PHE A 454 TYR 0.018 0.002 TYR B 114 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7481 (tmtt) cc_final: 0.7156 (tptp) REVERT: A 180 MET cc_start: 0.8810 (mmt) cc_final: 0.8055 (mmt) REVERT: A 229 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 238 GLN cc_start: 0.6722 (tp-100) cc_final: 0.6180 (tp40) REVERT: A 260 MET cc_start: 0.7446 (ptp) cc_final: 0.7233 (ptm) REVERT: A 410 TYR cc_start: 0.8427 (t80) cc_final: 0.8099 (t80) REVERT: A 432 ILE cc_start: 0.8872 (mt) cc_final: 0.8450 (mt) REVERT: A 563 LEU cc_start: 0.8577 (pt) cc_final: 0.7661 (tt) REVERT: B 133 THR cc_start: 0.7710 (p) cc_final: 0.7507 (p) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1705 time to fit residues: 37.6007 Evaluate side-chains 137 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.160 Angle : 0.604 10.940 8619 Z= 0.304 Chirality : 0.039 0.155 966 Planarity : 0.004 0.070 1048 Dihedral : 5.547 45.332 945 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.31), residues: 758 helix: 0.44 (0.27), residues: 366 sheet: -2.34 (0.47), residues: 97 loop : -1.78 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 458 HIS 0.005 0.001 HIS C 111 PHE 0.024 0.001 PHE A 427 TYR 0.016 0.001 TYR B 114 ARG 0.002 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7476 (tmtt) cc_final: 0.7123 (tptp) REVERT: A 180 MET cc_start: 0.8807 (mmt) cc_final: 0.8154 (mmt) REVERT: A 229 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 238 GLN cc_start: 0.6705 (tp-100) cc_final: 0.6049 (mm-40) REVERT: A 432 ILE cc_start: 0.8839 (mt) cc_final: 0.8399 (mt) REVERT: A 563 LEU cc_start: 0.8579 (pt) cc_final: 0.7687 (tt) REVERT: B 126 ASP cc_start: 0.8491 (m-30) cc_final: 0.8258 (m-30) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1643 time to fit residues: 36.1584 Evaluate side-chains 136 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.208 Angle : 0.660 12.700 8619 Z= 0.331 Chirality : 0.041 0.156 966 Planarity : 0.004 0.071 1048 Dihedral : 6.040 51.249 945 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.31), residues: 758 helix: 0.40 (0.27), residues: 359 sheet: -2.46 (0.47), residues: 97 loop : -1.68 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 271 HIS 0.006 0.002 HIS C 111 PHE 0.025 0.002 PHE A 427 TYR 0.020 0.002 TYR A 267 ARG 0.002 0.000 ARG C 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.7487 (tmtt) cc_final: 0.7140 (tptp) REVERT: A 229 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 563 LEU cc_start: 0.8615 (pt) cc_final: 0.7772 (tt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1661 time to fit residues: 36.2228 Evaluate side-chains 138 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.0370 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.181337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162756 restraints weight = 11484.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166857 restraints weight = 7207.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169799 restraints weight = 4961.065| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6326 Z= 0.155 Angle : 0.605 10.448 8619 Z= 0.303 Chirality : 0.039 0.157 966 Planarity : 0.004 0.068 1048 Dihedral : 5.822 47.898 945 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 758 helix: 0.49 (0.27), residues: 362 sheet: -2.42 (0.47), residues: 97 loop : -1.56 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 458 HIS 0.003 0.001 HIS C 111 PHE 0.030 0.001 PHE A 287 TYR 0.021 0.001 TYR A 267 ARG 0.002 0.000 ARG A 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.57 seconds wall clock time: 36 minutes 2.41 seconds (2162.41 seconds total)