Starting phenix.real_space_refine on Wed Feb 14 17:48:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d3y_27168/02_2024/8d3y_27168_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 58 5.16 5 Be 1 3.05 5 C 6340 2.51 5 N 1646 2.21 5 O 1850 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9898 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7341 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 41, 'TRANS': 940} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2311 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Time building chain proxies: 5.95, per 1000 atoms: 0.60 Number of scatterers: 9898 At special positions: 0 Unit cell: (141.48, 122.04, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 F 3 9.00 O 1850 8.00 N 1646 7.00 C 6340 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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: 4.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 11 sheets defined 39.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 65 removed outlier: 4.250A pdb=" N ALA A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.267A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 83' Processing helix chain 'A' and resid 91 through 110 Processing helix chain 'A' and resid 118 through 142 removed outlier: 3.791A pdb=" N GLY A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.513A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.572A pdb=" N VAL A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.992A pdb=" N VAL A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 4.199A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 359' Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 501 through 507 removed outlier: 5.812A pdb=" N ASP A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.770A pdb=" N GLU A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 611 through 621 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.696A pdb=" N LEU A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.711A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 745 through 772 removed outlier: 3.739A pdb=" N THR A 771 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 772 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 785 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'A' and resid 807 through 813 removed outlier: 3.991A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'A' and resid 847 through 864 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 877 through 880 No H-bonds generated for 'chain 'A' and resid 877 through 880' Processing helix chain 'A' and resid 898 through 926 removed outlier: 3.981A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 937 No H-bonds generated for 'chain 'A' and resid 934 through 937' Processing helix chain 'A' and resid 942 through 959 removed outlier: 4.015A pdb=" N PHE A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1001 removed outlier: 3.837A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 981 " --> pdb=" O TRP A 978 " (cutoff:3.500A) Proline residue: A 983 - end of helix Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'B' and resid 34 through 60 removed outlier: 3.692A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.884A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'G' and resid 37 through 57 Processing sheet with id= A, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.520A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.918A pdb=" N THR A 243 " --> pdb=" O HIS A 199 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 247 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 195 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.408A pdb=" N CYS A 201 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 602 through 604 Processing sheet with id= F, first strand: chain 'A' and resid 380 through 383 Processing sheet with id= G, first strand: chain 'A' and resid 544 through 550 removed outlier: 4.001A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 494 " --> pdb=" O HIS A 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 468 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 654 through 656 removed outlier: 7.092A pdb=" N VAL A 679 " --> pdb=" O ILE A 655 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 508 through 511 removed outlier: 6.766A pdb=" N LEU A 573 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE A 511 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE A 575 " --> pdb=" O ILE A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 87 through 91 removed outlier: 8.823A pdb=" N ILE B 88 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS B 298 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE B 90 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU B 300 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 299 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 272 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 301 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 270 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 176 through 179 removed outlier: 3.691A pdb=" N ILE B 176 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 260 " --> pdb=" O PHE B 230 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 918 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: 3.02 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3224 1.34 - 1.46: 2195 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 10099 Sorted by residual: bond pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 1.231 1.807 -0.576 2.00e-02 2.50e+03 8.30e+02 bond pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 1.529 1.263 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" OD1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.737 1.528 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" F1 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" F2 BFD A 366 " pdb="BE BFD A 366 " ideal model delta sigma weight residual 1.535 1.513 0.022 2.00e-02 2.50e+03 1.27e+00 ... (remaining 10094 not shown) Histogram of bond angle deviations from ideal: 66.96 - 80.37: 1 80.37 - 93.79: 0 93.79 - 107.20: 314 107.20 - 120.61: 9773 120.61 - 134.02: 3631 Bond angle restraints: 13719 Sorted by residual: angle pdb=" O BFD A 366 " pdb=" C BFD A 366 " pdb=" N LYS A 367 " ideal model delta sigma weight residual 123.00 66.96 56.04 1.60e+00 3.91e-01 1.23e+03 angle pdb=" CA BFD A 366 " pdb=" C BFD A 366 " pdb=" O BFD A 366 " ideal model delta sigma weight residual 120.80 94.22 26.58 1.70e+00 3.46e-01 2.45e+02 angle pdb=" CA BFD A 366 " pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " ideal model delta sigma weight residual 112.84 131.42 -18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" CB BFD A 366 " pdb=" CG BFD A 366 " pdb=" OD2 BFD A 366 " ideal model delta sigma weight residual 118.96 102.03 16.93 3.00e+00 1.11e-01 3.19e+01 angle pdb=" CB MET A 581 " pdb=" CG MET A 581 " pdb=" SD MET A 581 " ideal model delta sigma weight residual 112.70 122.54 -9.84 3.00e+00 1.11e-01 1.08e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5099 17.64 - 35.29: 729 35.29 - 52.93: 188 52.93 - 70.58: 30 70.58 - 88.22: 12 Dihedral angle restraints: 6058 sinusoidal: 2327 harmonic: 3731 Sorted by residual: dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 49 " pdb=" CB CYS A 49 " ideal model delta sinusoidal sigma weight residual 93.00 165.45 -72.45 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CA ILE A 285 " pdb=" C ILE A 285 " pdb=" N THR A 286 " pdb=" CA THR A 286 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLY B 30 " pdb=" C GLY B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1174 0.045 - 0.089: 335 0.089 - 0.134: 73 0.134 - 0.178: 2 0.178 - 0.223: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CB ILE A 926 " pdb=" CA ILE A 926 " pdb=" CG1 ILE A 926 " pdb=" CG2 ILE A 926 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR A 233 " pdb=" CA THR A 233 " pdb=" OG1 THR A 233 " pdb=" CG2 THR A 233 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET B 121 " pdb=" N MET B 121 " pdb=" C MET B 121 " pdb=" CB MET B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1582 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BFD A 366 " 0.222 2.00e-02 2.50e+03 3.06e-01 9.38e+02 pdb=" C BFD A 366 " -0.495 2.00e-02 2.50e+03 pdb=" O BFD A 366 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 367 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 73 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 74 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 430 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 431 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.022 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 864 2.74 - 3.28: 10212 3.28 - 3.82: 15966 3.82 - 4.36: 17949 4.36 - 4.90: 31035 Nonbonded interactions: 76026 Sorted by model distance: nonbonded pdb=" O THR A 607 " pdb=" OG1 THR A 683 " model vdw 2.198 2.440 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 45 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR A 892 " pdb=" O SER B 62 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.258 2.440 nonbonded pdb=" O ARG B 150 " pdb=" OH TYR B 242 " model vdw 2.264 2.440 ... (remaining 76021 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.870 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.200 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.576 10099 Z= 0.374 Angle : 0.814 56.037 13719 Z= 0.443 Chirality : 0.041 0.223 1585 Planarity : 0.008 0.306 1766 Dihedral : 17.343 88.219 3655 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.19 % Allowed : 34.00 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.14 (0.24), residues: 1289 helix: 1.24 (0.24), residues: 517 sheet: -0.56 (0.47), residues: 123 loop : -1.12 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 896 HIS 0.002 0.001 HIS A 909 PHE 0.019 0.001 PHE A 296 TYR 0.010 0.001 TYR G 32 ARG 0.011 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.223 Fit side-chains REVERT: A 973 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (pp) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.1681 time to fit residues: 36.7250 Evaluate side-chains 134 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 973 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 140 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN A 895 GLN A 900 GLN B 69 GLN B 82 GLN G 31 HIS G 35 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10099 Z= 0.184 Angle : 0.527 7.341 13719 Z= 0.274 Chirality : 0.040 0.139 1585 Planarity : 0.004 0.041 1766 Dihedral : 4.059 46.701 1389 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.80 % Allowed : 31.72 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.10 (0.24), residues: 1289 helix: 1.26 (0.23), residues: 512 sheet: -0.66 (0.47), residues: 125 loop : -1.03 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 896 HIS 0.002 0.001 HIS A 547 PHE 0.015 0.001 PHE B 230 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 1.238 Fit side-chains REVERT: A 260 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 341 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7929 (mtp) REVERT: A 524 MET cc_start: 0.5921 (tmm) cc_final: 0.5273 (tmm) REVERT: B 229 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: B 275 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6170 (pt0) outliers start: 40 outliers final: 21 residues processed: 166 average time/residue: 0.1585 time to fit residues: 41.5946 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.0070 chunk 97 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10099 Z= 0.151 Angle : 0.515 7.517 13719 Z= 0.262 Chirality : 0.040 0.138 1585 Planarity : 0.004 0.042 1766 Dihedral : 3.837 43.344 1387 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.18 % Allowed : 32.76 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.16 (0.24), residues: 1289 helix: 1.23 (0.24), residues: 511 sheet: -0.77 (0.46), residues: 130 loop : -1.06 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 155 HIS 0.002 0.000 HIS A 547 PHE 0.013 0.001 PHE B 123 TYR 0.009 0.001 TYR A 121 ARG 0.002 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.121 Fit side-chains REVERT: A 283 GLN cc_start: 0.5747 (OUTLIER) cc_final: 0.5398 (mp10) REVERT: A 524 MET cc_start: 0.6025 (tmm) cc_final: 0.5418 (tmm) REVERT: B 229 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: B 275 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6198 (pt0) outliers start: 44 outliers final: 22 residues processed: 175 average time/residue: 0.1584 time to fit residues: 43.6016 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0470 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10099 Z= 0.237 Angle : 0.544 7.341 13719 Z= 0.279 Chirality : 0.041 0.137 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.909 33.077 1387 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 6.36 % Allowed : 30.77 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.29 (0.24), residues: 1289 helix: 1.12 (0.24), residues: 512 sheet: -0.82 (0.42), residues: 147 loop : -1.14 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 977 HIS 0.002 0.001 HIS A 909 PHE 0.014 0.001 PHE G 44 TYR 0.010 0.001 TYR A 892 ARG 0.002 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 141 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 524 MET cc_start: 0.5957 (tmm) cc_final: 0.5627 (tmm) REVERT: A 973 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 223 LYS cc_start: 0.7910 (tptt) cc_final: 0.7603 (tptt) REVERT: B 229 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 272 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6989 (tp) REVERT: B 275 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6207 (pt0) outliers start: 67 outliers final: 45 residues processed: 189 average time/residue: 0.1715 time to fit residues: 49.4298 Evaluate side-chains 185 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10099 Z= 0.189 Angle : 0.540 10.175 13719 Z= 0.271 Chirality : 0.041 0.149 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.824 29.543 1387 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 5.98 % Allowed : 31.53 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.26 (0.24), residues: 1289 helix: 1.12 (0.24), residues: 513 sheet: -0.91 (0.42), residues: 140 loop : -1.08 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 977 HIS 0.002 0.001 HIS A 547 PHE 0.013 0.001 PHE A 783 TYR 0.012 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 142 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 524 MET cc_start: 0.6041 (tmm) cc_final: 0.5740 (tmm) REVERT: A 973 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 123 PHE cc_start: 0.8388 (m-80) cc_final: 0.8095 (m-80) REVERT: B 229 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6675 (m-80) REVERT: B 272 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6923 (tp) REVERT: B 275 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6221 (pt0) outliers start: 63 outliers final: 48 residues processed: 189 average time/residue: 0.1623 time to fit residues: 47.7360 Evaluate side-chains 189 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10099 Z= 0.160 Angle : 0.522 8.997 13719 Z= 0.263 Chirality : 0.040 0.153 1585 Planarity : 0.004 0.041 1766 Dihedral : 3.702 24.082 1387 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 5.51 % Allowed : 32.38 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.16 (0.24), residues: 1289 helix: 1.17 (0.24), residues: 515 sheet: -0.70 (0.46), residues: 125 loop : -1.04 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 977 HIS 0.001 0.000 HIS A 610 PHE 0.012 0.001 PHE A 783 TYR 0.014 0.001 TYR A 532 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 139 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 973 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 223 LYS cc_start: 0.7982 (tptt) cc_final: 0.7661 (tptt) REVERT: B 229 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: B 275 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6367 (pt0) outliers start: 58 outliers final: 47 residues processed: 181 average time/residue: 0.1733 time to fit residues: 50.2025 Evaluate side-chains 185 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN G 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10099 Z= 0.156 Angle : 0.528 8.487 13719 Z= 0.263 Chirality : 0.040 0.160 1585 Planarity : 0.004 0.042 1766 Dihedral : 3.607 21.835 1387 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 5.60 % Allowed : 32.19 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.14 (0.24), residues: 1289 helix: 1.18 (0.24), residues: 516 sheet: -0.78 (0.43), residues: 135 loop : -0.99 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.001 0.000 HIS A 610 PHE 0.015 0.001 PHE G 44 TYR 0.014 0.001 TYR A 532 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 138 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 973 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (pp) REVERT: B 57 MET cc_start: 0.8197 (tmm) cc_final: 0.7980 (tmm) REVERT: B 123 PHE cc_start: 0.8390 (m-80) cc_final: 0.8087 (m-80) REVERT: B 223 LYS cc_start: 0.8030 (tptt) cc_final: 0.7711 (tptt) REVERT: B 229 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: B 275 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6321 (pt0) outliers start: 59 outliers final: 47 residues processed: 183 average time/residue: 0.1652 time to fit residues: 47.5397 Evaluate side-chains 184 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 134 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10099 Z= 0.191 Angle : 0.541 8.277 13719 Z= 0.268 Chirality : 0.041 0.195 1585 Planarity : 0.004 0.042 1766 Dihedral : 3.640 24.058 1387 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 5.32 % Allowed : 32.38 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.19 (0.24), residues: 1289 helix: 1.15 (0.24), residues: 515 sheet: -0.80 (0.43), residues: 135 loop : -1.03 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.001 0.000 HIS A 483 PHE 0.014 0.001 PHE G 44 TYR 0.013 0.001 TYR A 532 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 973 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8345 (pp) REVERT: B 223 LYS cc_start: 0.7959 (tptt) cc_final: 0.7692 (tptt) REVERT: B 229 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: B 275 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6330 (pt0) outliers start: 56 outliers final: 51 residues processed: 178 average time/residue: 0.1599 time to fit residues: 44.8407 Evaluate side-chains 188 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 0.0040 chunk 119 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10099 Z= 0.140 Angle : 0.535 8.140 13719 Z= 0.263 Chirality : 0.040 0.195 1585 Planarity : 0.004 0.042 1766 Dihedral : 3.505 21.024 1387 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 4.65 % Allowed : 33.14 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.14 (0.24), residues: 1289 helix: 1.11 (0.24), residues: 529 sheet: -0.72 (0.43), residues: 135 loop : -0.99 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 977 HIS 0.001 0.000 HIS A 388 PHE 0.014 0.001 PHE G 44 TYR 0.017 0.001 TYR A 532 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 142 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 973 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (pp) REVERT: B 123 PHE cc_start: 0.8469 (m-80) cc_final: 0.8221 (m-80) REVERT: B 223 LYS cc_start: 0.7956 (tptt) cc_final: 0.7683 (tptt) REVERT: B 229 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: B 275 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6320 (pt0) outliers start: 49 outliers final: 45 residues processed: 179 average time/residue: 0.1641 time to fit residues: 46.4401 Evaluate side-chains 185 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 102 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10099 Z= 0.139 Angle : 0.537 8.006 13719 Z= 0.265 Chirality : 0.040 0.192 1585 Planarity : 0.004 0.043 1766 Dihedral : 3.449 19.779 1387 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 3.99 % Allowed : 33.81 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.10 (0.24), residues: 1289 helix: 1.16 (0.24), residues: 529 sheet: -0.70 (0.43), residues: 135 loop : -0.98 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 155 HIS 0.001 0.000 HIS A 413 PHE 0.013 0.001 PHE G 44 TYR 0.026 0.001 TYR G 32 ARG 0.003 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 973 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (pp) REVERT: B 223 LYS cc_start: 0.7960 (tptt) cc_final: 0.7695 (tptt) REVERT: B 229 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: B 275 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6190 (pt0) outliers start: 42 outliers final: 35 residues processed: 174 average time/residue: 0.1660 time to fit residues: 44.7795 Evaluate side-chains 174 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111093 restraints weight = 16784.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111638 restraints weight = 12913.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112295 restraints weight = 11404.019| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10099 Z= 0.215 Angle : 0.572 9.497 13719 Z= 0.282 Chirality : 0.041 0.209 1585 Planarity : 0.004 0.043 1766 Dihedral : 3.546 24.513 1387 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 4.56 % Allowed : 33.05 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.17 (0.24), residues: 1289 helix: 1.11 (0.24), residues: 523 sheet: -0.71 (0.42), residues: 147 loop : -1.02 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 977 HIS 0.001 0.001 HIS A 483 PHE 0.015 0.001 PHE G 44 TYR 0.018 0.001 TYR G 32 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.61 seconds wall clock time: 39 minutes 50.86 seconds (2390.86 seconds total)