Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:04:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_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_21369/02_2023/6vrk_21369_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrk_21369/02_2023/6vrk_21369_updated.pdb" } resolution = 4.1 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= -0.001 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 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 chiralities: 2 Time building chain proxies: 4.04, per 1000 atoms: 0.66 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: 2.31 Conformation dependent library (CDL) restraints added in 958.1 milliseconds 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: 0.74 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: 1.52 Time building geometry restraints manager: 2.52 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=" C TRP A 458 " pdb=" N ALA A 459 " pdb=" CA ALA A 459 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.78e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 3409 23.60 - 47.20: 161 47.20 - 70.80: 11 70.80 - 94.40: 8 94.40 - 118.00: 2 Dihedral angle restraints: 3591 sinusoidal: 1377 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=" C01 RFS A 704 " pdb=" C02 RFS A 704 " pdb=" N03 RFS A 704 " pdb=" C04 RFS A 704 " ideal model delta sinusoidal sigma weight residual -53.69 64.31 -118.00 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 623 0.031 - 0.062: 247 0.062 - 0.093: 67 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA ARG B 121 " pdb=" N ARG B 121 " pdb=" C ARG B 121 " pdb=" CB ARG B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE C 114 " pdb=" N ILE C 114 " pdb=" C ILE C 114 " pdb=" CB ILE C 114 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE A 587 " pdb=" N ILE A 587 " pdb=" C ILE A 587 " pdb=" CB ILE A 587 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (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 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. 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: 0.010 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 13.870 Check model and map are aligned: 0.090 Process input model: 19.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 6326 Z= 0.213 Angle : 0.613 11.612 8619 Z= 0.334 Chirality : 0.037 0.154 966 Planarity : 0.004 0.065 1048 Dihedral : 13.758 118.000 2176 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.00 % 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: -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 *********************** 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 : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1856 time to fit residues: 52.0854 Evaluate side-chains 157 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9328 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 C 109 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2251 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= 0.208 Angle : 0.633 13.863 8619 Z= 0.320 Chirality : 0.040 0.157 966 Planarity : 0.005 0.070 1048 Dihedral : 5.423 74.782 860 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.46 % 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: -2.24 (0.29), residues: 758 helix: -0.14 (0.26), residues: 357 sheet: -2.79 (0.44), residues: 90 loop : -2.67 (0.34), residues: 311 *********************** 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 187 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.1576 time to fit residues: 40.3714 Evaluate side-chains 150 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0580 time to fit residues: 1.0755 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 6326 Z= 0.217 Angle : 0.638 11.065 8619 Z= 0.324 Chirality : 0.041 0.168 966 Planarity : 0.005 0.070 1048 Dihedral : 4.853 46.710 860 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.15 % 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: -2.00 (0.30), residues: 758 helix: 0.05 (0.27), residues: 358 sheet: -2.82 (0.45), residues: 92 loop : -2.49 (0.34), residues: 308 *********************** 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 175 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1743 time to fit residues: 41.4276 Evaluate side-chains 140 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8866 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6326 Z= 0.190 Angle : 0.626 10.844 8619 Z= 0.316 Chirality : 0.040 0.181 966 Planarity : 0.004 0.069 1048 Dihedral : 4.780 45.190 860 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 0.00 % 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: -1.92 (0.30), residues: 758 helix: 0.04 (0.27), residues: 363 sheet: -2.56 (0.46), residues: 90 loop : -2.47 (0.35), residues: 305 *********************** 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 176 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1573 time to fit residues: 38.1036 Evaluate side-chains 141 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8855 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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** C 57 GLN B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 6326 Z= 0.262 Angle : 0.682 10.163 8619 Z= 0.349 Chirality : 0.042 0.168 966 Planarity : 0.005 0.074 1048 Dihedral : 5.187 48.193 860 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.00 % 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: -1.93 (0.30), residues: 758 helix: 0.07 (0.27), residues: 358 sheet: -2.74 (0.44), residues: 94 loop : -2.42 (0.35), residues: 306 *********************** 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 177 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1639 time to fit residues: 39.4135 Evaluate side-chains 141 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8799 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.213 Angle : 0.645 10.327 8619 Z= 0.328 Chirality : 0.041 0.170 966 Planarity : 0.004 0.070 1048 Dihedral : 5.079 46.517 860 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.00 % 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: -1.77 (0.30), residues: 758 helix: 0.16 (0.27), residues: 352 sheet: -2.65 (0.44), residues: 95 loop : -2.23 (0.35), residues: 311 *********************** 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 176 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1678 time to fit residues: 40.6036 Evaluate side-chains 138 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8627 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 562 GLN C 57 GLN C 109 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6326 Z= 0.173 Angle : 0.618 10.289 8619 Z= 0.313 Chirality : 0.040 0.163 966 Planarity : 0.004 0.069 1048 Dihedral : 4.859 45.617 860 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 0.15 % 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: -1.61 (0.30), residues: 758 helix: 0.24 (0.27), residues: 358 sheet: -2.60 (0.44), residues: 95 loop : -2.10 (0.36), residues: 305 *********************** 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 174 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1633 time to fit residues: 38.9198 Evaluate side-chains 144 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9457 ------------------------------------------------------------------------------- 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: 0.2980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6326 Z= 0.164 Angle : 0.620 12.273 8619 Z= 0.311 Chirality : 0.039 0.163 966 Planarity : 0.004 0.068 1048 Dihedral : 4.750 45.311 860 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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: -1.51 (0.31), residues: 758 helix: 0.33 (0.28), residues: 360 sheet: -2.61 (0.45), residues: 95 loop : -2.04 (0.36), residues: 303 *********************** 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 169 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1565 time to fit residues: 36.4969 Evaluate side-chains 141 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9100 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** C 57 GLN C 111 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 6326 Z= 0.152 Angle : 0.618 10.693 8619 Z= 0.308 Chirality : 0.039 0.159 966 Planarity : 0.004 0.067 1048 Dihedral : 4.673 45.032 860 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % 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: -1.34 (0.31), residues: 758 helix: 0.42 (0.28), residues: 358 sheet: -2.49 (0.46), residues: 95 loop : -1.89 (0.37), residues: 305 *********************** 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 168 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1881 time to fit residues: 44.2253 Evaluate side-chains 138 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8975 ------------------------------------------------------------------------------- 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: 0.5980 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS C 57 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6326 Z= 0.186 Angle : 0.638 10.622 8619 Z= 0.319 Chirality : 0.040 0.161 966 Planarity : 0.004 0.068 1048 Dihedral : 4.827 46.767 860 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.00 % 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: -1.39 (0.31), residues: 758 helix: 0.36 (0.28), residues: 357 sheet: -2.51 (0.46), residues: 95 loop : -1.88 (0.37), residues: 306 ********************** 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 175 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1632 time to fit residues: 39.4646 Evaluate side-chains 142 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9765 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 C 57 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.185980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164941 restraints weight = 11792.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.169532 restraints weight = 7401.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.172941 restraints weight = 5129.399| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4284 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= 0.154 Angle : 0.623 10.760 8619 Z= 0.312 Chirality : 0.039 0.158 966 Planarity : 0.004 0.067 1048 Dihedral : 4.682 46.135 860 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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: -1.39 (0.31), residues: 758 helix: 0.36 (0.28), residues: 361 sheet: -2.41 (0.47), residues: 95 loop : -1.94 (0.37), residues: 302 =============================================================================== Job complete usr+sys time: 1823.02 seconds wall clock time: 34 minutes 29.05 seconds (2069.05 seconds total)