Starting phenix.real_space_refine on Sat Mar 16 07:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt6_26112/03_2024/7tt6_26112.pdb" } resolution = 4.3 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= 0.005 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 4562 2.51 5 N 1221 2.21 5 O 1398 1.98 5 H 6839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14047 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2271 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 7 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7687 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 21, 'TRANS': 480} Chain breaks: 3 Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 484 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "D" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2223 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 3 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1382 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 6.71, per 1000 atoms: 0.48 Number of scatterers: 14047 At special positions: 0 Unit cell: (93.4223, 95.57, 135.301, 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) S 27 16.00 O 1398 8.00 N 1221 7.00 C 4562 6.00 H 6839 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 23.7% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 280 through 289 removed outlier: 4.129A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.877A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 removed outlier: 4.324A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.650A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.476A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 165 through 189 removed outlier: 3.529A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.802A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'P' and resid 1039 through 1046 removed outlier: 4.078A pdb=" N HIS P1062 " --> pdb=" O MET P1046 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 1039 through 1046 removed outlier: 4.078A pdb=" N HIS P1062 " --> pdb=" O MET P1046 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA P1291 " --> pdb=" O GLU P1279 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA P1294 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 430 " --> pdb=" O ALA P1294 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.968A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.620A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.700A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.689A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1206 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: 5.32 Time building geometry restraints manager: 11.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6839 1.04 - 1.24: 909 1.24 - 1.44: 2453 1.44 - 1.64: 3960 1.64 - 1.84: 50 Bond restraints: 14211 Sorted by residual: bond pdb=" CB TRP A 739 " pdb=" CG TRP A 739 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.69e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.65e+00 bond pdb=" CA THR D 186 " pdb=" C THR D 186 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.30e-02 5.92e+03 1.53e+00 bond pdb=" C THR A 720 " pdb=" O THR A 720 " ideal model delta sigma weight residual 1.235 1.251 -0.015 1.29e-02 6.01e+03 1.44e+00 ... (remaining 14206 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.62: 175 105.62 - 112.76: 15625 112.76 - 119.91: 4164 119.91 - 127.05: 5377 127.05 - 134.20: 85 Bond angle restraints: 25426 Sorted by residual: angle pdb=" N PHE A 478 " pdb=" CA PHE A 478 " pdb=" C PHE A 478 " ideal model delta sigma weight residual 113.12 107.69 5.43 1.25e+00 6.40e-01 1.89e+01 angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.96 102.81 7.15 1.68e+00 3.54e-01 1.81e+01 angle pdb=" CA CYS A 690 " pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " ideal model delta sigma weight residual 114.40 123.72 -9.32 2.30e+00 1.89e-01 1.64e+01 angle pdb=" C ARG A 734 " pdb=" N THR A 735 " pdb=" CA THR A 735 " ideal model delta sigma weight residual 122.59 116.46 6.13 1.57e+00 4.06e-01 1.53e+01 angle pdb=" CA CYS A 700 " pdb=" CB CYS A 700 " pdb=" SG CYS A 700 " ideal model delta sigma weight residual 114.40 122.69 -8.29 2.30e+00 1.89e-01 1.30e+01 ... (remaining 25421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6416 18.00 - 35.99: 217 35.99 - 53.99: 103 53.99 - 71.98: 38 71.98 - 89.98: 7 Dihedral angle restraints: 6781 sinusoidal: 3577 harmonic: 3204 Sorted by residual: dihedral pdb=" CA LEU A 377 " pdb=" C LEU A 377 " pdb=" N GLY A 378 " pdb=" CA GLY A 378 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR A 688 " pdb=" C TYR A 688 " pdb=" N GLU A 689 " pdb=" CA GLU A 689 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP P1270 " pdb=" C ASP P1270 " pdb=" N ASN P1271 " pdb=" CA ASN P1271 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 685 0.037 - 0.074: 227 0.074 - 0.110: 96 0.110 - 0.147: 31 0.147 - 0.184: 7 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE P1167 " pdb=" N ILE P1167 " pdb=" C ILE P1167 " pdb=" CB ILE P1167 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ARG D 223 " pdb=" N ARG D 223 " pdb=" C ARG D 223 " pdb=" CB ARG D 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 1043 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 167 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.89e+01 pdb=" C LEU D 167 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU D 167 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL D 168 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 166 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C ARG D 166 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG D 166 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU D 167 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P1168 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLU P1168 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU P1168 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO P1169 " 0.024 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 258 2.08 - 2.71: 23218 2.71 - 3.34: 37093 3.34 - 3.97: 48065 3.97 - 4.60: 74500 Nonbonded interactions: 183134 Sorted by model distance: nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.453 1.850 nonbonded pdb=" OE1 GLN D 209 " pdb="HH21 ARG D 212 " model vdw 1.551 1.850 nonbonded pdb=" OD2 ASP A 582 " pdb=" HG1 THR A 588 " model vdw 1.558 1.850 nonbonded pdb=" OD1 ASP A 569 " pdb=" H ASN A 606 " model vdw 1.566 1.850 nonbonded pdb=" OD1 ASP D 136 " pdb=" H GLN D 138 " model vdw 1.576 1.850 ... (remaining 183129 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 3.570 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 46.790 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.005 0.040 7372 Z= 0.315 Angle : 0.910 9.320 9983 Z= 0.556 Chirality : 0.047 0.184 1046 Planarity : 0.006 0.070 1309 Dihedral : 10.729 89.977 2628 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 879 helix: -1.55 (0.31), residues: 178 sheet: 1.23 (0.25), residues: 345 loop : 0.42 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 449 HIS 0.008 0.003 HIS A 555 PHE 0.016 0.002 PHE A 791 TYR 0.023 0.002 TYR A 585 ARG 0.011 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1260 MET cc_start: 0.4627 (mtm) cc_final: 0.4335 (mpp) REVERT: A 307 ASP cc_start: 0.8373 (m-30) cc_final: 0.8078 (m-30) REVERT: A 422 ASN cc_start: 0.7854 (m-40) cc_final: 0.7568 (m-40) REVERT: A 542 GLN cc_start: 0.8887 (mt0) cc_final: 0.8669 (mm-40) REVERT: A 557 SER cc_start: 0.8992 (m) cc_final: 0.8619 (t) REVERT: A 633 THR cc_start: 0.8382 (p) cc_final: 0.8109 (p) REVERT: A 768 MET cc_start: 0.7980 (mtt) cc_final: 0.7521 (mtm) REVERT: A 783 LEU cc_start: 0.7923 (mt) cc_final: 0.7723 (mt) REVERT: A 805 ASN cc_start: 0.8545 (t0) cc_final: 0.7858 (p0) REVERT: D 127 PHE cc_start: 0.8668 (t80) cc_final: 0.8460 (t80) REVERT: D 208 THR cc_start: 0.9142 (t) cc_final: 0.8911 (t) REVERT: D 228 ASN cc_start: 0.8670 (m-40) cc_final: 0.8309 (m-40) REVERT: E 31 ASP cc_start: 0.8285 (m-30) cc_final: 0.7616 (p0) REVERT: E 41 ASN cc_start: 0.9062 (m-40) cc_final: 0.8727 (t0) REVERT: E 43 VAL cc_start: 0.9383 (t) cc_final: 0.9142 (t) REVERT: E 64 MET cc_start: 0.8471 (mtp) cc_final: 0.8247 (mtm) REVERT: E 80 GLN cc_start: 0.8626 (tp40) cc_final: 0.8297 (tp40) REVERT: E 81 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: E 95 PHE cc_start: 0.8396 (m-80) cc_final: 0.8146 (m-80) REVERT: E 103 ASN cc_start: 0.9095 (t0) cc_final: 0.8782 (t0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4533 time to fit residues: 173.2899 Evaluate side-chains 198 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN D 230 GLN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7372 Z= 0.181 Angle : 0.562 5.175 9983 Z= 0.318 Chirality : 0.043 0.180 1046 Planarity : 0.004 0.039 1309 Dihedral : 4.569 38.327 1003 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.27 % Allowed : 1.60 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 879 helix: 0.35 (0.37), residues: 182 sheet: 0.78 (0.24), residues: 373 loop : 0.53 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.004 0.001 HIS C 51 PHE 0.015 0.001 PHE A 738 TYR 0.019 0.001 TYR D 184 ARG 0.005 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1292 VAL cc_start: 0.8114 (p) cc_final: 0.7726 (m) REVERT: A 422 ASN cc_start: 0.8160 (m-40) cc_final: 0.7890 (m-40) REVERT: A 426 PHE cc_start: 0.8747 (t80) cc_final: 0.8435 (t80) REVERT: A 445 GLN cc_start: 0.8303 (pp30) cc_final: 0.7671 (pm20) REVERT: A 446 GLN cc_start: 0.8491 (mt0) cc_final: 0.8239 (mt0) REVERT: A 447 ASP cc_start: 0.7818 (t0) cc_final: 0.7609 (t0) REVERT: A 542 GLN cc_start: 0.9007 (mt0) cc_final: 0.8684 (mm-40) REVERT: A 557 SER cc_start: 0.8943 (m) cc_final: 0.8572 (t) REVERT: A 768 MET cc_start: 0.8179 (mtt) cc_final: 0.7895 (mtm) REVERT: D 84 ASP cc_start: 0.7784 (m-30) cc_final: 0.7266 (m-30) REVERT: D 117 MET cc_start: 0.9070 (tmm) cc_final: 0.8691 (pmm) REVERT: D 127 PHE cc_start: 0.8667 (t80) cc_final: 0.8442 (t80) REVERT: D 207 ASP cc_start: 0.7778 (m-30) cc_final: 0.7013 (m-30) REVERT: E 31 ASP cc_start: 0.8217 (m-30) cc_final: 0.7621 (p0) REVERT: E 38 LEU cc_start: 0.8426 (tt) cc_final: 0.8205 (tt) REVERT: E 41 ASN cc_start: 0.9107 (m-40) cc_final: 0.8662 (t0) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.4417 time to fit residues: 132.4790 Evaluate side-chains 193 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 87 optimal weight: 0.0050 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7097 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7372 Z= 0.127 Angle : 0.497 4.932 9983 Z= 0.277 Chirality : 0.042 0.164 1046 Planarity : 0.004 0.044 1309 Dihedral : 4.237 30.546 1003 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 879 helix: 0.93 (0.38), residues: 182 sheet: 0.53 (0.24), residues: 373 loop : 0.70 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.001 0.000 HIS A 533 PHE 0.014 0.001 PHE A 570 TYR 0.016 0.001 TYR D 184 ARG 0.009 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1292 VAL cc_start: 0.8031 (p) cc_final: 0.7595 (m) REVERT: P 1298 TYR cc_start: 0.7198 (t80) cc_final: 0.6984 (t80) REVERT: A 304 MET cc_start: 0.8112 (mtp) cc_final: 0.7795 (tpp) REVERT: A 445 GLN cc_start: 0.8275 (pp30) cc_final: 0.7914 (pm20) REVERT: A 447 ASP cc_start: 0.7773 (t0) cc_final: 0.7503 (t0) REVERT: A 542 GLN cc_start: 0.9023 (mt0) cc_final: 0.8777 (mm-40) REVERT: A 557 SER cc_start: 0.8978 (m) cc_final: 0.8615 (t) REVERT: A 648 PHE cc_start: 0.9012 (p90) cc_final: 0.8791 (p90) REVERT: A 740 ASP cc_start: 0.6774 (m-30) cc_final: 0.6432 (m-30) REVERT: A 768 MET cc_start: 0.8172 (mtt) cc_final: 0.7910 (mtm) REVERT: D 84 ASP cc_start: 0.7734 (m-30) cc_final: 0.7132 (m-30) REVERT: D 127 PHE cc_start: 0.8658 (t80) cc_final: 0.8403 (t80) REVERT: D 207 ASP cc_start: 0.7561 (m-30) cc_final: 0.7033 (m-30) REVERT: E 31 ASP cc_start: 0.8186 (m-30) cc_final: 0.7623 (p0) REVERT: E 101 LEU cc_start: 0.8432 (tp) cc_final: 0.8168 (tp) REVERT: E 104 ILE cc_start: 0.8904 (pt) cc_final: 0.8537 (mm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.4148 time to fit residues: 121.0648 Evaluate side-chains 188 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7372 Z= 0.266 Angle : 0.548 8.783 9983 Z= 0.308 Chirality : 0.042 0.159 1046 Planarity : 0.004 0.045 1309 Dihedral : 4.299 20.559 1003 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 879 helix: 0.70 (0.37), residues: 189 sheet: 0.24 (0.24), residues: 373 loop : 0.38 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.011 0.001 HIS A 533 PHE 0.024 0.001 PHE A 738 TYR 0.017 0.001 TYR D 184 ARG 0.004 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8631 (mmt) cc_final: 0.8170 (mmt) REVERT: A 422 ASN cc_start: 0.7876 (m-40) cc_final: 0.7669 (t0) REVERT: A 445 GLN cc_start: 0.8322 (pp30) cc_final: 0.7851 (pm20) REVERT: A 557 SER cc_start: 0.9050 (m) cc_final: 0.8678 (t) REVERT: A 648 PHE cc_start: 0.9201 (p90) cc_final: 0.8892 (p90) REVERT: A 674 TYR cc_start: 0.8325 (m-80) cc_final: 0.8071 (m-10) REVERT: A 720 THR cc_start: 0.8889 (p) cc_final: 0.8634 (p) REVERT: D 84 ASP cc_start: 0.7643 (m-30) cc_final: 0.7142 (m-30) REVERT: D 228 ASN cc_start: 0.8389 (m110) cc_final: 0.8146 (m110) REVERT: E 31 ASP cc_start: 0.8252 (m-30) cc_final: 0.7692 (p0) REVERT: E 101 LEU cc_start: 0.8453 (tp) cc_final: 0.8164 (tp) REVERT: E 104 ILE cc_start: 0.8915 (pt) cc_final: 0.8580 (mm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.4192 time to fit residues: 112.5186 Evaluate side-chains 177 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 80.0000 chunk 64 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7372 Z= 0.141 Angle : 0.486 6.600 9983 Z= 0.267 Chirality : 0.041 0.153 1046 Planarity : 0.004 0.064 1309 Dihedral : 4.138 21.129 1003 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 879 helix: 1.06 (0.38), residues: 189 sheet: 0.23 (0.24), residues: 370 loop : 0.35 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 576 HIS 0.005 0.001 HIS A 533 PHE 0.011 0.001 PHE P1278 TYR 0.015 0.001 TYR D 184 ARG 0.011 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1278 PHE cc_start: 0.6734 (t80) cc_final: 0.6405 (t80) REVERT: P 1279 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8206 (tm-30) REVERT: A 369 MET cc_start: 0.8562 (mmt) cc_final: 0.8240 (mmt) REVERT: A 422 ASN cc_start: 0.7942 (m-40) cc_final: 0.7728 (t0) REVERT: A 445 GLN cc_start: 0.8400 (pp30) cc_final: 0.7880 (pm20) REVERT: A 446 GLN cc_start: 0.8408 (mt0) cc_final: 0.7721 (mm-40) REVERT: A 557 SER cc_start: 0.8985 (m) cc_final: 0.8602 (t) REVERT: A 630 LEU cc_start: 0.8730 (tp) cc_final: 0.8486 (tp) REVERT: A 709 ASN cc_start: 0.8120 (t0) cc_final: 0.7513 (t0) REVERT: A 727 ASP cc_start: 0.8778 (p0) cc_final: 0.8454 (p0) REVERT: A 740 ASP cc_start: 0.6736 (m-30) cc_final: 0.6360 (m-30) REVERT: D 84 ASP cc_start: 0.7661 (m-30) cc_final: 0.7020 (m-30) REVERT: D 127 PHE cc_start: 0.8670 (t80) cc_final: 0.8397 (t80) REVERT: D 228 ASN cc_start: 0.8368 (m110) cc_final: 0.8093 (m110) REVERT: E 31 ASP cc_start: 0.8238 (m-30) cc_final: 0.7943 (m-30) REVERT: E 101 LEU cc_start: 0.8436 (tp) cc_final: 0.8166 (tp) REVERT: E 104 ILE cc_start: 0.8922 (pt) cc_final: 0.8608 (mm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4333 time to fit residues: 121.0217 Evaluate side-chains 178 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7372 Z= 0.380 Angle : 0.616 6.101 9983 Z= 0.349 Chirality : 0.043 0.220 1046 Planarity : 0.005 0.065 1309 Dihedral : 4.601 25.577 1003 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 879 helix: 0.17 (0.36), residues: 190 sheet: -0.07 (0.24), residues: 363 loop : -0.25 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 739 HIS 0.004 0.001 HIS A 533 PHE 0.025 0.002 PHE A 586 TYR 0.021 0.002 TYR E 75 ARG 0.010 0.001 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1271 ASN cc_start: 0.8620 (p0) cc_final: 0.8412 (p0) REVERT: A 284 ILE cc_start: 0.9238 (mm) cc_final: 0.8770 (tp) REVERT: A 557 SER cc_start: 0.9065 (m) cc_final: 0.8704 (t) REVERT: A 630 LEU cc_start: 0.8755 (tp) cc_final: 0.8524 (tp) REVERT: A 648 PHE cc_start: 0.9271 (p90) cc_final: 0.9042 (p90) REVERT: A 740 ASP cc_start: 0.7006 (m-30) cc_final: 0.6720 (m-30) REVERT: D 84 ASP cc_start: 0.7670 (m-30) cc_final: 0.7076 (m-30) REVERT: D 127 PHE cc_start: 0.8705 (t80) cc_final: 0.8449 (t80) REVERT: D 196 ASN cc_start: 0.9072 (m-40) cc_final: 0.8527 (t0) REVERT: D 228 ASN cc_start: 0.8466 (m110) cc_final: 0.8140 (m110) REVERT: E 31 ASP cc_start: 0.8473 (m-30) cc_final: 0.7874 (p0) REVERT: E 90 THR cc_start: 0.9344 (p) cc_final: 0.9008 (m) REVERT: E 101 LEU cc_start: 0.8585 (tp) cc_final: 0.8237 (tp) REVERT: E 104 ILE cc_start: 0.8907 (pt) cc_final: 0.8543 (mm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.4287 time to fit residues: 111.7398 Evaluate side-chains 174 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7372 Z= 0.149 Angle : 0.491 5.180 9983 Z= 0.272 Chirality : 0.042 0.167 1046 Planarity : 0.004 0.048 1309 Dihedral : 4.231 20.655 1003 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 879 helix: 0.81 (0.38), residues: 189 sheet: -0.06 (0.24), residues: 371 loop : -0.09 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.014 0.001 PHE P1278 TYR 0.014 0.001 TYR D 184 ARG 0.005 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9214 (mm) cc_final: 0.8690 (tp) REVERT: A 287 LEU cc_start: 0.9378 (pp) cc_final: 0.8986 (pp) REVERT: A 369 MET cc_start: 0.8611 (mmt) cc_final: 0.8322 (mmt) REVERT: A 557 SER cc_start: 0.9102 (m) cc_final: 0.8742 (t) REVERT: A 630 LEU cc_start: 0.8738 (tp) cc_final: 0.8441 (tp) REVERT: A 740 ASP cc_start: 0.6564 (m-30) cc_final: 0.6325 (m-30) REVERT: D 84 ASP cc_start: 0.7676 (m-30) cc_final: 0.6998 (m-30) REVERT: D 228 ASN cc_start: 0.8382 (m110) cc_final: 0.8056 (m110) REVERT: E 31 ASP cc_start: 0.8285 (m-30) cc_final: 0.7830 (p0) REVERT: E 104 ILE cc_start: 0.8949 (pt) cc_final: 0.8633 (mm) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.4209 time to fit residues: 114.0873 Evaluate side-chains 177 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7372 Z= 0.223 Angle : 0.510 4.881 9983 Z= 0.287 Chirality : 0.042 0.173 1046 Planarity : 0.004 0.053 1309 Dihedral : 4.191 16.969 1003 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 879 helix: 0.59 (0.38), residues: 189 sheet: -0.12 (0.24), residues: 372 loop : -0.21 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.016 0.001 PHE D 144 TYR 0.016 0.001 TYR D 184 ARG 0.005 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9202 (mm) cc_final: 0.8583 (tp) REVERT: A 307 ASP cc_start: 0.8371 (t70) cc_final: 0.8132 (t0) REVERT: A 445 GLN cc_start: 0.8505 (pp30) cc_final: 0.8128 (pp30) REVERT: A 557 SER cc_start: 0.9103 (m) cc_final: 0.8760 (t) REVERT: A 630 LEU cc_start: 0.8729 (tp) cc_final: 0.8391 (tp) REVERT: A 740 ASP cc_start: 0.6576 (m-30) cc_final: 0.6279 (m-30) REVERT: A 783 LEU cc_start: 0.7935 (mm) cc_final: 0.7570 (mm) REVERT: D 84 ASP cc_start: 0.7654 (m-30) cc_final: 0.6965 (m-30) REVERT: D 232 GLU cc_start: 0.8839 (mp0) cc_final: 0.8507 (mp0) REVERT: E 31 ASP cc_start: 0.8333 (m-30) cc_final: 0.7861 (p0) REVERT: E 101 LEU cc_start: 0.8409 (tp) cc_final: 0.8034 (tp) REVERT: E 104 ILE cc_start: 0.8970 (pt) cc_final: 0.8721 (mm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.4071 time to fit residues: 104.0931 Evaluate side-chains 168 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7372 Z= 0.194 Angle : 0.496 5.009 9983 Z= 0.276 Chirality : 0.042 0.171 1046 Planarity : 0.004 0.054 1309 Dihedral : 4.172 17.547 1003 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 879 helix: 0.62 (0.38), residues: 190 sheet: -0.15 (0.25), residues: 372 loop : -0.09 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.015 0.001 PHE P1278 TYR 0.014 0.001 TYR D 184 ARG 0.004 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9199 (mm) cc_final: 0.8576 (tp) REVERT: A 304 MET cc_start: 0.7763 (tpp) cc_final: 0.7322 (tpp) REVERT: A 445 GLN cc_start: 0.8547 (pp30) cc_final: 0.8138 (pp30) REVERT: A 557 SER cc_start: 0.9115 (m) cc_final: 0.8752 (t) REVERT: A 630 LEU cc_start: 0.8695 (tp) cc_final: 0.8413 (tp) REVERT: A 740 ASP cc_start: 0.6413 (m-30) cc_final: 0.6139 (m-30) REVERT: A 783 LEU cc_start: 0.7939 (mm) cc_final: 0.7715 (mm) REVERT: D 84 ASP cc_start: 0.7637 (m-30) cc_final: 0.6951 (m-30) REVERT: D 232 GLU cc_start: 0.8797 (mp0) cc_final: 0.8450 (mp0) REVERT: E 31 ASP cc_start: 0.8334 (m-30) cc_final: 0.7854 (p0) REVERT: E 101 LEU cc_start: 0.8428 (tp) cc_final: 0.8097 (tp) REVERT: E 104 ILE cc_start: 0.8981 (pt) cc_final: 0.8748 (mm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.4284 time to fit residues: 110.1509 Evaluate side-chains 171 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7372 Z= 0.224 Angle : 0.506 5.024 9983 Z= 0.283 Chirality : 0.042 0.170 1046 Planarity : 0.004 0.055 1309 Dihedral : 4.210 18.175 1003 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 879 helix: 0.53 (0.38), residues: 190 sheet: -0.12 (0.25), residues: 370 loop : -0.17 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 PHE 0.020 0.001 PHE P1296 TYR 0.016 0.001 TYR D 184 ARG 0.005 0.001 ARG D 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.9203 (mm) cc_final: 0.8605 (tp) REVERT: A 445 GLN cc_start: 0.8591 (pp30) cc_final: 0.8211 (pp30) REVERT: A 557 SER cc_start: 0.9132 (m) cc_final: 0.8777 (t) REVERT: A 630 LEU cc_start: 0.8702 (tp) cc_final: 0.8441 (tp) REVERT: A 648 PHE cc_start: 0.9260 (p90) cc_final: 0.8994 (p90) REVERT: A 704 ASP cc_start: 0.8251 (t0) cc_final: 0.8027 (t0) REVERT: A 740 ASP cc_start: 0.6496 (m-30) cc_final: 0.6223 (m-30) REVERT: D 84 ASP cc_start: 0.7674 (m-30) cc_final: 0.6973 (m-30) REVERT: D 130 VAL cc_start: 0.8502 (t) cc_final: 0.8211 (p) REVERT: D 196 ASN cc_start: 0.9100 (m-40) cc_final: 0.8602 (t0) REVERT: E 31 ASP cc_start: 0.8345 (m-30) cc_final: 0.7853 (p0) REVERT: E 101 LEU cc_start: 0.8319 (tp) cc_final: 0.8078 (tp) REVERT: E 104 ILE cc_start: 0.8998 (pt) cc_final: 0.8690 (mm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.4147 time to fit residues: 107.7325 Evaluate side-chains 171 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095327 restraints weight = 41155.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100364 restraints weight = 18312.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103513 restraints weight = 11786.442| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7372 Z= 0.297 Angle : 0.552 4.833 9983 Z= 0.310 Chirality : 0.042 0.168 1046 Planarity : 0.005 0.093 1309 Dihedral : 4.414 19.861 1003 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.27), residues: 879 helix: 0.15 (0.37), residues: 190 sheet: -0.20 (0.25), residues: 370 loop : -0.41 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 739 HIS 0.002 0.001 HIS D 139 PHE 0.016 0.001 PHE A 738 TYR 0.017 0.001 TYR D 184 ARG 0.011 0.001 ARG E 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3837.39 seconds wall clock time: 67 minutes 59.68 seconds (4079.68 seconds total)