Starting phenix.real_space_refine on Thu Feb 15 21:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsb_12563/02_2024/7nsb_12563.pdb" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8725 2.51 5 N 2277 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 11": "OE1" <-> "OE2" Residue "a PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ASP 95": "OD1" <-> "OD2" Residue "a TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 316": "OD1" <-> "OD2" Residue "a ASP 342": "OD1" <-> "OD2" Residue "a TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 535": "NH1" <-> "NH2" Residue "a PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 596": "OD1" <-> "OD2" Residue "a GLU 610": "OE1" <-> "OE2" Residue "a PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 694": "NH1" <-> "NH2" Residue "a ARG 768": "NH1" <-> "NH2" Residue "a TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 805": "OE1" <-> "OE2" Residue "a ARG 855": "NH1" <-> "NH2" Residue "a ARG 857": "NH1" <-> "NH2" Residue "a GLU 877": "OE1" <-> "OE2" Residue "a TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 894": "NH1" <-> "NH2" Residue "a GLU 931": "OE1" <-> "OE2" Residue "a ARG 944": "NH1" <-> "NH2" Residue "g TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 279": "OD1" <-> "OD2" Residue "g ASP 304": "OD1" <-> "OD2" Residue "g PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "g ASP 399": "OD1" <-> "OD2" Residue "g ARG 458": "NH1" <-> "NH2" Residue "g ARG 500": "NH1" <-> "NH2" Residue "g GLU 509": "OE1" <-> "OE2" Residue "g ASP 547": "OD1" <-> "OD2" Residue "g ASP 570": "OD1" <-> "OD2" Residue "g PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 597": "NH1" <-> "NH2" Residue "g ASP 643": "OD1" <-> "OD2" Residue "g TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 142": "OD1" <-> "OD2" Residue "7 ARG 160": "NH1" <-> "NH2" Residue "7 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 500": "NH1" <-> "NH2" Residue "7 TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 567": "OD1" <-> "OD2" Residue "7 ASP 570": "OD1" <-> "OD2" Residue "7 ASP 643": "OD1" <-> "OD2" Residue "7 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 91": "NH1" <-> "NH2" Residue "h PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 145": "NH1" <-> "NH2" Residue "h ARG 283": "NH1" <-> "NH2" Residue "h ASP 315": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13474 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4376 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 19, 'TRANS': 548} Chain breaks: 9 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 165 Chain: "g" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3173 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "7" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4075 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 18, 'TRANS': 512} Chain breaks: 11 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 168 Chain: "h" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1850 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 5 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ASN:plan1': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 7.24, per 1000 atoms: 0.54 Number of scatterers: 13474 At special positions: 0 Unit cell: (126.4, 169.06, 102.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2417 8.00 N 2277 7.00 C 8725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3398 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 16 sheets defined 35.4% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'a' and resid 7 through 17 removed outlier: 4.710A pdb=" N GLU a 11 " --> pdb=" O ASP a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.060A pdb=" N GLN a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN a 24 " --> pdb=" O TYR a 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 19 through 24' Processing helix chain 'a' and resid 26 through 36 removed outlier: 3.942A pdb=" N LEU a 30 " --> pdb=" O VAL a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 45 Processing helix chain 'a' and resid 70 through 81 removed outlier: 4.051A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 105 removed outlier: 3.626A pdb=" N TYR a 103 " --> pdb=" O GLN a 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE a 104 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 115 Processing helix chain 'a' and resid 318 through 321 No H-bonds generated for 'chain 'a' and resid 318 through 321' Processing helix chain 'a' and resid 497 through 503 Processing helix chain 'a' and resid 597 through 613 removed outlier: 4.255A pdb=" N LYS a 603 " --> pdb=" O GLY a 599 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP a 604 " --> pdb=" O TYR a 600 " (cutoff:3.500A) Processing helix chain 'a' and resid 709 through 724 Processing helix chain 'a' and resid 728 through 741 Processing helix chain 'a' and resid 751 through 766 removed outlier: 3.893A pdb=" N VAL a 755 " --> pdb=" O GLU a 751 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE a 756 " --> pdb=" O SER a 752 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU a 766 " --> pdb=" O GLN a 762 " (cutoff:3.500A) Processing helix chain 'a' and resid 768 through 782 removed outlier: 3.575A pdb=" N ILE a 772 " --> pdb=" O ARG a 768 " (cutoff:3.500A) Processing helix chain 'a' and resid 785 through 794 Processing helix chain 'a' and resid 799 through 802 No H-bonds generated for 'chain 'a' and resid 799 through 802' Processing helix chain 'a' and resid 804 through 822 removed outlier: 4.043A pdb=" N GLU a 809 " --> pdb=" O GLU a 805 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA a 813 " --> pdb=" O GLU a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 829 through 845 removed outlier: 3.982A pdb=" N ILE a 834 " --> pdb=" O ILE a 830 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU a 835 " --> pdb=" O GLU a 831 " (cutoff:3.500A) Processing helix chain 'a' and resid 852 through 869 removed outlier: 3.722A pdb=" N SER a 859 " --> pdb=" O ARG a 855 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY a 860 " --> pdb=" O ASP a 856 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN a 861 " --> pdb=" O ARG a 857 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU a 862 " --> pdb=" O PHE a 858 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU a 868 " --> pdb=" O ASN a 864 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU a 869 " --> pdb=" O VAL a 865 " (cutoff:3.500A) Processing helix chain 'a' and resid 880 through 885 Processing helix chain 'a' and resid 888 through 907 removed outlier: 4.048A pdb=" N PHE a 896 " --> pdb=" O GLN a 892 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN a 897 " --> pdb=" O GLU a 893 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN a 901 " --> pdb=" O GLN a 897 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU a 907 " --> pdb=" O ILE a 903 " (cutoff:3.500A) Processing helix chain 'a' and resid 915 through 932 removed outlier: 3.739A pdb=" N TYR a 932 " --> pdb=" O THR a 928 " (cutoff:3.500A) Processing helix chain 'a' and resid 951 through 956 Processing helix chain 'g' and resid 31 through 43 removed outlier: 3.530A pdb=" N LEU g 35 " --> pdb=" O GLN g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 53 Processing helix chain 'g' and resid 263 through 278 removed outlier: 4.333A pdb=" N LYS g 269 " --> pdb=" O LEU g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 576 through 581 Processing helix chain '7' and resid 29 through 43 Processing helix chain '7' and resid 46 through 54 removed outlier: 3.909A pdb=" N LEU 7 53 " --> pdb=" O ALA 7 49 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU 7 54 " --> pdb=" O ASN 7 50 " (cutoff:3.500A) Processing helix chain '7' and resid 65 through 75 Processing helix chain '7' and resid 83 through 87 Processing helix chain '7' and resid 99 through 106 removed outlier: 5.507A pdb=" N GLN 7 103 " --> pdb=" O SER 7 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG 7 104 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 118 through 136 removed outlier: 3.867A pdb=" N GLN 7 130 " --> pdb=" O GLN 7 126 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU 7 131 " --> pdb=" O TYR 7 127 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET 7 132 " --> pdb=" O LEU 7 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER 7 133 " --> pdb=" O GLN 7 129 " (cutoff:3.500A) Processing helix chain '7' and resid 143 through 167 removed outlier: 4.178A pdb=" N ASN 7 150 " --> pdb=" O ALA 7 146 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE 7 166 " --> pdb=" O ILE 7 162 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE 7 167 " --> pdb=" O PHE 7 163 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 205 removed outlier: 3.814A pdb=" N LEU 7 186 " --> pdb=" O ALA 7 182 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS 7 190 " --> pdb=" O LEU 7 186 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE 7 195 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 229 removed outlier: 3.815A pdb=" N LEU 7 229 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 237 Processing helix chain '7' and resid 243 through 252 Processing helix chain '7' and resid 263 through 278 removed outlier: 3.800A pdb=" N GLN 7 278 " --> pdb=" O TYR 7 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 44 Processing helix chain 'h' and resid 89 through 100 removed outlier: 3.723A pdb=" N LEU h 94 " --> pdb=" O PRO h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 112 Processing helix chain 'h' and resid 120 through 128 Processing helix chain 'h' and resid 131 through 143 Processing helix chain 'h' and resid 146 through 151 Processing helix chain 'h' and resid 193 through 208 Processing helix chain 'h' and resid 223 through 236 Processing helix chain 'h' and resid 243 through 249 Processing helix chain 'h' and resid 273 through 278 removed outlier: 4.355A pdb=" N TYR h 278 " --> pdb=" O LEU h 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 280 through 299 removed outlier: 4.230A pdb=" N ILE h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA h 287 " --> pdb=" O ARG h 283 " (cutoff:3.500A) Processing helix chain 'h' and resid 301 through 308 Processing helix chain 'h' and resid 418 through 423 Processing helix chain 'h' and resid 428 through 444 removed outlier: 3.706A pdb=" N HIS h 444 " --> pdb=" O GLU h 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 337 through 340 removed outlier: 5.325A pdb=" N HIS a 346 " --> pdb=" O SER a 340 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR a 345 " --> pdb=" O THR a 585 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR a 585 " --> pdb=" O THR a 345 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN a 581 " --> pdb=" O PRO a 349 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER a 582 " --> pdb=" O LEU a 409 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR a 400 " --> pdb=" O PHE a 545 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR a 404 " --> pdb=" O CYS a 541 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP a 537 " --> pdb=" O VAL a 408 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY a 548 " --> pdb=" O ASP a 565 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE a 550 " --> pdb=" O PHE a 563 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 386 through 390 removed outlier: 3.725A pdb=" N ILE a 424 " --> pdb=" O TYR a 512 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY a 511 " --> pdb=" O THR a 520 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS a 513 " --> pdb=" O LEU a 518 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU a 518 " --> pdb=" O CYS a 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g' and resid 328 through 333 removed outlier: 4.000A pdb=" N PHE g 329 " --> pdb=" O ALA g 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER g 333 " --> pdb=" O TYR g 338 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR g 338 " --> pdb=" O SER g 333 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE g 352 " --> pdb=" O CYS g 367 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP g 356 " --> pdb=" O ILE g 363 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE g 363 " --> pdb=" O ASP g 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'g' and resid 376 through 380 removed outlier: 5.352A pdb=" N TYR g 385 " --> pdb=" O SER g 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 460 through 465 removed outlier: 5.616A pdb=" N TRP g 473 " --> pdb=" O PHE g 465 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU g 482 " --> pdb=" O SER g 478 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA g 483 " --> pdb=" O LEU g 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE g 495 " --> pdb=" O VAL g 485 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER g 487 " --> pdb=" O SER g 493 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER g 493 " --> pdb=" O SER g 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 546 through 551 removed outlier: 5.143A pdb=" N ASP g 547 " --> pdb=" O MET g 560 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TYR g 556 " --> pdb=" O SER g 551 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL g 565 " --> pdb=" O THR g 561 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA g 596 " --> pdb=" O VAL g 568 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP g 570 " --> pdb=" O ARG g 594 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG g 594 " --> pdb=" O ASP g 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 606 through 609 removed outlier: 4.102A pdb=" N CYS g 606 " --> pdb=" O SER g 633 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU g 634 " --> pdb=" O GLU g 638 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU g 638 " --> pdb=" O LEU g 634 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN g 651 " --> pdb=" O MET g 641 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP g 643 " --> pdb=" O LEU g 649 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU g 649 " --> pdb=" O ASP g 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 663 through 668 removed outlier: 6.469A pdb=" N ARG g 664 " --> pdb=" O GLY g 677 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY g 677 " --> pdb=" O ARG g 664 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER g 678 " --> pdb=" O LYS g 682 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS g 682 " --> pdb=" O SER g 678 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP g 687 " --> pdb=" O LEU g 693 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU g 693 " --> pdb=" O ASP g 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 715 through 721 removed outlier: 5.838A pdb=" N MET g 727 " --> pdb=" O ASN g 721 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU g 726 " --> pdb=" O ILE g 742 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS g 738 " --> pdb=" O SER g 730 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY g 732 " --> pdb=" O LYS g 736 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS g 736 " --> pdb=" O GLY g 732 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE g 737 " --> pdb=" O THR g 319 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR g 319 " --> pdb=" O ILE g 737 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE g 739 " --> pdb=" O TRP g 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '7' and resid 329 through 333 removed outlier: 3.801A pdb=" N PHE 7 329 " --> pdb=" O ALA 7 342 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR 7 331 " --> pdb=" O ALA 7 340 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR 7 338 " --> pdb=" O SER 7 333 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR 7 353 " --> pdb=" O SER 7 341 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE 7 352 " --> pdb=" O CYS 7 367 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP 7 356 " --> pdb=" O ILE 7 363 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE 7 363 " --> pdb=" O ASP 7 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 376 through 380 removed outlier: 3.809A pdb=" N TYR 7 376 " --> pdb=" O CYS 7 389 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR 7 385 " --> pdb=" O SER 7 380 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR 7 396 " --> pdb=" O ALA 7 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '7' and resid 460 through 465 removed outlier: 4.427A pdb=" N CYS 7 461 " --> pdb=" O GLY 7 477 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP 7 473 " --> pdb=" O PHE 7 465 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL 7 476 " --> pdb=" O ILE 7 484 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 7 484 " --> pdb=" O VAL 7 476 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 7 478 " --> pdb=" O GLU 7 482 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU 7 482 " --> pdb=" O SER 7 478 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA 7 483 " --> pdb=" O LEU 7 497 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE 7 495 " --> pdb=" O VAL 7 485 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER 7 487 " --> pdb=" O SER 7 493 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER 7 493 " --> pdb=" O SER 7 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '7' and resid 546 through 551 removed outlier: 5.236A pdb=" N ASP 7 547 " --> pdb=" O MET 7 560 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR 7 556 " --> pdb=" O SER 7 551 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL 7 565 " --> pdb=" O THR 7 561 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA 7 596 " --> pdb=" O VAL 7 568 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP 7 570 " --> pdb=" O ARG 7 594 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG 7 594 " --> pdb=" O ASP 7 570 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '7' and resid 606 through 609 removed outlier: 4.827A pdb=" N CYS 7 606 " --> pdb=" O SER 7 633 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER 7 608 " --> pdb=" O LEU 7 631 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU 7 631 " --> pdb=" O SER 7 608 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL 7 630 " --> pdb=" O TRP 7 642 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 7 634 " --> pdb=" O GLU 7 638 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU 7 638 " --> pdb=" O LEU 7 634 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN 7 651 " --> pdb=" O MET 7 641 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP 7 643 " --> pdb=" O LEU 7 649 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU 7 649 " --> pdb=" O ASP 7 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '7' and resid 663 through 668 removed outlier: 5.946A pdb=" N ARG 7 664 " --> pdb=" O GLY 7 677 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 7 678 " --> pdb=" O LYS 7 682 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS 7 682 " --> pdb=" O SER 7 678 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP 7 687 " --> pdb=" O LEU 7 693 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU 7 693 " --> pdb=" O ASP 7 687 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 715 through 721 removed outlier: 4.201A pdb=" N ASN 7 721 " --> pdb=" O MET 7 727 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET 7 727 " --> pdb=" O ASN 7 721 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU 7 726 " --> pdb=" O ILE 7 742 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE 7 742 " --> pdb=" O GLU 7 726 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY 7 732 " --> pdb=" O LYS 7 736 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS 7 736 " --> pdb=" O GLY 7 732 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE 7 737 " --> pdb=" O THR 7 319 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR 7 319 " --> pdb=" O ILE 7 737 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE 7 739 " --> pdb=" O TRP 7 317 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1650 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: 4.61 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4276 1.34 - 1.46: 2112 1.46 - 1.57: 7289 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 13760 Sorted by residual: bond pdb=" CB PRO h 314 " pdb=" CG PRO h 314 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.69e+00 bond pdb=" CG1 ILE 7 742 " pdb=" CD1 ILE 7 742 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" C PRO g 295 " pdb=" N PRO g 296 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" CG1 ILE g 683 " pdb=" CD1 ILE g 683 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.10e-01 bond pdb=" CB LEU a 895 " pdb=" CG LEU a 895 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 8.89e-01 ... (remaining 13755 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 255 106.04 - 113.04: 7530 113.04 - 120.04: 4649 120.04 - 127.04: 6153 127.04 - 134.04: 148 Bond angle restraints: 18735 Sorted by residual: angle pdb=" C VAL a 108 " pdb=" N ASN a 109 " pdb=" CA ASN a 109 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ASP a 847 " pdb=" N THR a 848 " pdb=" CA THR a 848 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C PRO g 587 " pdb=" N LYS g 588 " pdb=" CA LYS g 588 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N ASP a 516 " pdb=" CA ASP a 516 " pdb=" C ASP a 516 " ideal model delta sigma weight residual 114.56 110.68 3.88 1.27e+00 6.20e-01 9.32e+00 angle pdb=" N LYS g 725 " pdb=" CA LYS g 725 " pdb=" CB LYS g 725 " ideal model delta sigma weight residual 113.65 109.71 3.94 1.47e+00 4.63e-01 7.17e+00 ... (remaining 18730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 7271 17.05 - 34.10: 682 34.10 - 51.15: 115 51.15 - 68.20: 13 68.20 - 85.25: 10 Dihedral angle restraints: 8091 sinusoidal: 2872 harmonic: 5219 Sorted by residual: dihedral pdb=" CA GLU 7 726 " pdb=" C GLU 7 726 " pdb=" N MET 7 727 " pdb=" CA MET 7 727 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN 7 721 " pdb=" C ASN 7 721 " pdb=" N PRO 7 722 " pdb=" CA PRO 7 722 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU 7 634 " pdb=" C LEU 7 634 " pdb=" N GLN 7 635 " pdb=" CA GLN 7 635 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 8088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1298 0.034 - 0.068: 611 0.068 - 0.102: 195 0.102 - 0.135: 81 0.135 - 0.169: 13 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CA VAL 7 395 " pdb=" N VAL 7 395 " pdb=" C VAL 7 395 " pdb=" CB VAL 7 395 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ASN a 109 " pdb=" N ASN a 109 " pdb=" C ASN a 109 " pdb=" CB ASN a 109 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE g 683 " pdb=" N ILE g 683 " pdb=" C ILE g 683 " pdb=" CB ILE g 683 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2195 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 7 189 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ARG 7 189 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG 7 189 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS 7 190 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO g 295 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO g 296 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO g 296 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO g 296 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS a 531 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO a 532 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO a 532 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 532 " -0.034 5.00e-02 4.00e+02 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1840 2.75 - 3.29: 13141 3.29 - 3.83: 20419 3.83 - 4.36: 22934 4.36 - 4.90: 40683 Nonbonded interactions: 99017 Sorted by model distance: nonbonded pdb=" OE1 GLN g 270 " pdb=" NE2 GLN 7 275 " model vdw 2.214 2.520 nonbonded pdb=" OE1 GLU 7 153 " pdb=" OH TYR 7 252 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR a 28 " pdb=" O TYR h 46 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR g 669 " pdb=" O ASN g 745 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR a 426 " pdb=" O CYS a 541 " model vdw 2.265 2.440 ... (remaining 99012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 5.540 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.040 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13760 Z= 0.269 Angle : 0.701 8.742 18735 Z= 0.379 Chirality : 0.045 0.169 2198 Planarity : 0.005 0.074 2359 Dihedral : 13.751 85.246 4693 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -2.03 (0.21), residues: 1707 helix: 0.88 (0.23), residues: 593 sheet: -1.46 (0.30), residues: 294 loop : -3.16 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP g 686 HIS 0.011 0.001 HIS 7 486 PHE 0.012 0.001 PHE 7 379 TYR 0.014 0.001 TYR a 574 ARG 0.004 0.000 ARG 7 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.576 Fit side-chains REVERT: a 31 TRP cc_start: 0.7440 (t-100) cc_final: 0.6985 (t-100) REVERT: a 683 GLU cc_start: 0.8592 (pm20) cc_final: 0.8267 (pm20) REVERT: 7 200 ASP cc_start: 0.9078 (t70) cc_final: 0.8757 (t0) REVERT: 7 226 SER cc_start: 0.9002 (p) cc_final: 0.8585 (p) REVERT: 7 355 TYR cc_start: 0.8951 (m-10) cc_final: 0.8495 (m-10) REVERT: 7 636 ASP cc_start: 0.7234 (m-30) cc_final: 0.6903 (t70) REVERT: 7 675 MET cc_start: 0.8523 (ptp) cc_final: 0.8191 (ptp) REVERT: 7 726 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7200 (tm-30) REVERT: h 245 MET cc_start: 0.8440 (mmm) cc_final: 0.8185 (mmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2176 time to fit residues: 62.1245 Evaluate side-chains 147 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 567 ASN ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 HIS 7 714 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13760 Z= 0.226 Angle : 0.612 9.308 18735 Z= 0.315 Chirality : 0.043 0.160 2198 Planarity : 0.004 0.074 2359 Dihedral : 5.140 22.796 1880 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 1.03 % Allowed : 9.60 % Favored : 89.36 % 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: -1.78 (0.21), residues: 1707 helix: 1.12 (0.23), residues: 599 sheet: -1.29 (0.31), residues: 294 loop : -3.07 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 308 PHE 0.010 0.001 PHE 7 209 TYR 0.023 0.001 TYR h 229 ARG 0.002 0.000 ARG 7 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.743 Fit side-chains REVERT: a 31 TRP cc_start: 0.7417 (t-100) cc_final: 0.7038 (t-100) REVERT: a 422 ILE cc_start: 0.9241 (mp) cc_final: 0.8862 (mt) REVERT: a 683 GLU cc_start: 0.8607 (pm20) cc_final: 0.8250 (pm20) REVERT: 7 200 ASP cc_start: 0.9095 (t70) cc_final: 0.8800 (t0) REVERT: 7 355 TYR cc_start: 0.8917 (m-10) cc_final: 0.8533 (m-10) REVERT: 7 636 ASP cc_start: 0.7312 (m-30) cc_final: 0.6955 (t70) REVERT: 7 714 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6801 (p0) REVERT: h 46 TYR cc_start: 0.6461 (t80) cc_final: 0.6169 (t80) REVERT: h 245 MET cc_start: 0.8421 (mmm) cc_final: 0.8206 (mmt) outliers start: 14 outliers final: 11 residues processed: 171 average time/residue: 0.2188 time to fit residues: 58.6406 Evaluate side-chains 158 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 714 ASN Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 0.0570 chunk 127 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 714 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13760 Z= 0.204 Angle : 0.591 9.187 18735 Z= 0.304 Chirality : 0.043 0.156 2198 Planarity : 0.004 0.074 2359 Dihedral : 4.944 21.577 1880 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 1.62 % Allowed : 13.37 % Favored : 85.01 % 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: -1.62 (0.21), residues: 1707 helix: 1.26 (0.23), residues: 600 sheet: -1.19 (0.30), residues: 300 loop : -3.00 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.019 0.001 PHE 7 314 TYR 0.018 0.001 TYR h 229 ARG 0.002 0.000 ARG 7 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.660 Fit side-chains REVERT: a 31 TRP cc_start: 0.7401 (t-100) cc_final: 0.7058 (t-100) REVERT: a 422 ILE cc_start: 0.9314 (mp) cc_final: 0.8912 (mt) REVERT: a 683 GLU cc_start: 0.8612 (pm20) cc_final: 0.8227 (pm20) REVERT: g 32 LEU cc_start: 0.8025 (tt) cc_final: 0.7599 (tp) REVERT: 7 121 MET cc_start: 0.9164 (mmt) cc_final: 0.8905 (mmt) REVERT: 7 200 ASP cc_start: 0.9094 (t70) cc_final: 0.8802 (t0) REVERT: 7 355 TYR cc_start: 0.8885 (m-10) cc_final: 0.8516 (m-10) REVERT: 7 636 ASP cc_start: 0.7394 (m-30) cc_final: 0.6921 (t70) REVERT: h 46 TYR cc_start: 0.6273 (t80) cc_final: 0.5798 (t80) REVERT: h 245 MET cc_start: 0.8248 (mmm) cc_final: 0.7881 (mmt) outliers start: 22 outliers final: 14 residues processed: 177 average time/residue: 0.2215 time to fit residues: 61.1787 Evaluate side-chains 166 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 656 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13760 Z= 0.251 Angle : 0.605 8.514 18735 Z= 0.312 Chirality : 0.043 0.162 2198 Planarity : 0.004 0.074 2359 Dihedral : 4.987 22.292 1880 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 2.29 % Allowed : 14.40 % Favored : 83.31 % 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: -1.59 (0.21), residues: 1707 helix: 1.30 (0.23), residues: 595 sheet: -1.15 (0.30), residues: 302 loop : -2.99 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.011 0.001 PHE 7 209 TYR 0.016 0.001 TYR h 229 ARG 0.002 0.000 ARG 7 664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.536 Fit side-chains REVERT: a 31 TRP cc_start: 0.7552 (t-100) cc_final: 0.7202 (t-100) REVERT: a 422 ILE cc_start: 0.9223 (mp) cc_final: 0.8843 (mt) REVERT: 7 200 ASP cc_start: 0.9167 (t70) cc_final: 0.8836 (t0) REVERT: 7 355 TYR cc_start: 0.8906 (m-10) cc_final: 0.8542 (m-10) REVERT: 7 636 ASP cc_start: 0.7534 (m-30) cc_final: 0.7082 (t70) REVERT: h 46 TYR cc_start: 0.6482 (t80) cc_final: 0.6139 (t80) REVERT: h 245 MET cc_start: 0.8458 (mmm) cc_final: 0.8111 (mmt) outliers start: 31 outliers final: 27 residues processed: 176 average time/residue: 0.2137 time to fit residues: 59.0573 Evaluate side-chains 177 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 818 MET Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 107 ILE Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 656 GLN Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 116 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13760 Z= 0.200 Angle : 0.581 8.278 18735 Z= 0.300 Chirality : 0.042 0.159 2198 Planarity : 0.004 0.073 2359 Dihedral : 4.854 22.660 1880 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 2.66 % Allowed : 16.25 % Favored : 81.09 % 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: -1.41 (0.21), residues: 1707 helix: 1.42 (0.23), residues: 591 sheet: -1.09 (0.30), residues: 298 loop : -2.81 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.011 0.001 PHE 7 209 TYR 0.014 0.001 TYR h 229 ARG 0.002 0.000 ARG a 923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.575 Fit side-chains REVERT: a 31 TRP cc_start: 0.7509 (t-100) cc_final: 0.7194 (t-100) REVERT: a 422 ILE cc_start: 0.9238 (mp) cc_final: 0.8825 (mt) REVERT: a 683 GLU cc_start: 0.8421 (pm20) cc_final: 0.8101 (pm20) REVERT: g 32 LEU cc_start: 0.8030 (tt) cc_final: 0.7561 (tp) REVERT: g 639 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8479 (mt) REVERT: 7 121 MET cc_start: 0.9156 (mmt) cc_final: 0.8935 (mmt) REVERT: 7 200 ASP cc_start: 0.9139 (t70) cc_final: 0.8814 (t0) REVERT: 7 355 TYR cc_start: 0.8898 (m-10) cc_final: 0.8492 (m-10) REVERT: h 205 MET cc_start: 0.8135 (mmm) cc_final: 0.7566 (tpt) REVERT: h 245 MET cc_start: 0.8449 (mmm) cc_final: 0.8109 (mmt) outliers start: 36 outliers final: 28 residues processed: 190 average time/residue: 0.2218 time to fit residues: 65.3452 Evaluate side-chains 182 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 107 ILE Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13760 Z= 0.184 Angle : 0.566 9.106 18735 Z= 0.293 Chirality : 0.042 0.199 2198 Planarity : 0.004 0.072 2359 Dihedral : 4.686 22.089 1880 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.60 % Favored : 88.34 % Rotamer: Outliers : 3.03 % Allowed : 16.54 % Favored : 80.43 % 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: -1.29 (0.21), residues: 1707 helix: 1.50 (0.23), residues: 594 sheet: -0.82 (0.31), residues: 286 loop : -2.81 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.018 0.001 PHE 7 314 TYR 0.014 0.001 TYR h 229 ARG 0.002 0.000 ARG a 923 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.702 Fit side-chains REVERT: a 31 TRP cc_start: 0.7480 (t-100) cc_final: 0.7199 (t-100) REVERT: a 422 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8840 (mt) REVERT: a 683 GLU cc_start: 0.8449 (pm20) cc_final: 0.8068 (pm20) REVERT: g 639 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8471 (mt) REVERT: 7 200 ASP cc_start: 0.9140 (t70) cc_final: 0.8816 (t0) REVERT: 7 355 TYR cc_start: 0.8822 (m-10) cc_final: 0.8586 (m-10) REVERT: h 46 TYR cc_start: 0.6405 (t80) cc_final: 0.6176 (t80) REVERT: h 205 MET cc_start: 0.8111 (mmm) cc_final: 0.7521 (tpt) REVERT: h 245 MET cc_start: 0.8269 (mmm) cc_final: 0.7916 (mmt) outliers start: 41 outliers final: 32 residues processed: 186 average time/residue: 0.1989 time to fit residues: 59.1723 Evaluate side-chains 188 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 107 ILE Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 636 ASP Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 0.0020 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13760 Z= 0.165 Angle : 0.562 8.758 18735 Z= 0.289 Chirality : 0.042 0.171 2198 Planarity : 0.004 0.072 2359 Dihedral : 4.543 22.500 1880 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.19 % Favored : 88.75 % Rotamer: Outliers : 3.25 % Allowed : 17.13 % Favored : 79.62 % 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: -1.22 (0.21), residues: 1707 helix: 1.50 (0.23), residues: 605 sheet: -0.76 (0.31), residues: 287 loop : -2.79 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.010 0.001 PHE 7 209 TYR 0.021 0.001 TYR a 404 ARG 0.002 0.000 ARG h 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 1.638 Fit side-chains REVERT: a 31 TRP cc_start: 0.7451 (t-100) cc_final: 0.7185 (t-100) REVERT: a 422 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8817 (mt) REVERT: a 683 GLU cc_start: 0.8455 (pm20) cc_final: 0.8069 (pm20) REVERT: g 639 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8440 (mt) REVERT: 7 200 ASP cc_start: 0.9135 (t70) cc_final: 0.8814 (t0) REVERT: h 46 TYR cc_start: 0.6403 (t80) cc_final: 0.6190 (t80) REVERT: h 205 MET cc_start: 0.8086 (mmm) cc_final: 0.7478 (tpt) REVERT: h 245 MET cc_start: 0.8259 (mmm) cc_final: 0.7907 (mmt) outliers start: 44 outliers final: 32 residues processed: 191 average time/residue: 0.1984 time to fit residues: 60.3303 Evaluate side-chains 186 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 636 ASP Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 671 ASN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13760 Z= 0.248 Angle : 0.605 8.729 18735 Z= 0.312 Chirality : 0.043 0.161 2198 Planarity : 0.004 0.073 2359 Dihedral : 4.759 22.618 1880 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 3.25 % Allowed : 17.73 % Favored : 79.03 % 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: -1.21 (0.21), residues: 1707 helix: 1.58 (0.23), residues: 592 sheet: -0.86 (0.31), residues: 292 loop : -2.73 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.019 0.001 PHE 7 314 TYR 0.011 0.001 TYR h 229 ARG 0.002 0.000 ARG 7 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 1.743 Fit side-chains REVERT: a 31 TRP cc_start: 0.7548 (t-100) cc_final: 0.7206 (t-100) REVERT: a 422 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8833 (mt) REVERT: g 560 MET cc_start: 0.8525 (tpp) cc_final: 0.8220 (tpp) REVERT: g 639 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8482 (mt) REVERT: 7 121 MET cc_start: 0.9152 (mmt) cc_final: 0.8942 (mmt) REVERT: 7 200 ASP cc_start: 0.9166 (t70) cc_final: 0.8841 (t0) REVERT: 7 355 TYR cc_start: 0.9058 (m-10) cc_final: 0.8836 (m-10) REVERT: h 205 MET cc_start: 0.8125 (mmm) cc_final: 0.7525 (tpt) REVERT: h 245 MET cc_start: 0.8494 (mmm) cc_final: 0.7964 (mmp) outliers start: 44 outliers final: 37 residues processed: 186 average time/residue: 0.2105 time to fit residues: 61.6915 Evaluate side-chains 197 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 591 LEU Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 636 ASP Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 chunk 148 optimal weight: 0.0270 chunk 156 optimal weight: 0.0980 chunk 103 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 601 GLN ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13760 Z= 0.160 Angle : 0.562 8.764 18735 Z= 0.290 Chirality : 0.042 0.156 2198 Planarity : 0.004 0.071 2359 Dihedral : 4.506 23.037 1880 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.51 % Allowed : 18.91 % Favored : 78.58 % 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: -1.09 (0.21), residues: 1707 helix: 1.58 (0.23), residues: 605 sheet: -0.73 (0.30), residues: 290 loop : -2.67 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.013 0.001 PHE 7 332 TYR 0.011 0.001 TYR h 229 ARG 0.001 0.000 ARG h 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.622 Fit side-chains REVERT: a 31 TRP cc_start: 0.7477 (t-100) cc_final: 0.7166 (t-100) REVERT: a 422 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8803 (mt) REVERT: a 683 GLU cc_start: 0.8452 (pm20) cc_final: 0.8233 (pm20) REVERT: g 560 MET cc_start: 0.8330 (tpp) cc_final: 0.8063 (tpp) REVERT: g 639 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8391 (mt) REVERT: 7 200 ASP cc_start: 0.9143 (t70) cc_final: 0.8814 (t0) REVERT: 7 226 SER cc_start: 0.9110 (p) cc_final: 0.8718 (m) REVERT: 7 268 LEU cc_start: 0.9196 (mt) cc_final: 0.8991 (mp) REVERT: h 205 MET cc_start: 0.8059 (mmm) cc_final: 0.7434 (tpt) REVERT: h 245 MET cc_start: 0.8482 (mmm) cc_final: 0.7968 (mmp) outliers start: 34 outliers final: 31 residues processed: 178 average time/residue: 0.2067 time to fit residues: 58.5203 Evaluate side-chains 188 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 591 LEU Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 366 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 636 ASP Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 282 ASN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13760 Z= 0.169 Angle : 0.567 8.738 18735 Z= 0.292 Chirality : 0.042 0.156 2198 Planarity : 0.004 0.071 2359 Dihedral : 4.435 23.224 1880 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.88 % Allowed : 18.69 % Favored : 78.43 % 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: -1.10 (0.21), residues: 1707 helix: 1.54 (0.23), residues: 612 sheet: -0.71 (0.30), residues: 291 loop : -2.69 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.017 0.001 PHE 7 332 TYR 0.013 0.001 TYR 7 355 ARG 0.002 0.000 ARG a 923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.758 Fit side-chains REVERT: a 31 TRP cc_start: 0.7457 (t-100) cc_final: 0.7172 (t-100) REVERT: a 422 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8802 (mt) REVERT: a 683 GLU cc_start: 0.8489 (pm20) cc_final: 0.8250 (pm20) REVERT: g 639 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8412 (mt) REVERT: 7 200 ASP cc_start: 0.9148 (t70) cc_final: 0.8815 (t0) REVERT: 7 226 SER cc_start: 0.9091 (p) cc_final: 0.8733 (m) REVERT: h 205 MET cc_start: 0.8051 (mmm) cc_final: 0.7422 (tpt) REVERT: h 245 MET cc_start: 0.8491 (mmm) cc_final: 0.7974 (mmp) outliers start: 39 outliers final: 32 residues processed: 190 average time/residue: 0.2114 time to fit residues: 64.2944 Evaluate side-chains 195 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 29 ASP Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 282 ASN Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 591 LEU Chi-restraints excluded: chain g residue 600 VAL Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 366 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 636 ASP Chi-restraints excluded: chain 7 residue 680 ASP Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 0.0070 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101902 restraints weight = 25026.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104471 restraints weight = 14474.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106227 restraints weight = 10106.082| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13760 Z= 0.205 Angle : 0.591 9.165 18735 Z= 0.302 Chirality : 0.042 0.157 2198 Planarity : 0.004 0.072 2359 Dihedral : 4.525 24.056 1880 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 2.51 % Allowed : 19.20 % Favored : 78.29 % 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: -1.06 (0.21), residues: 1707 helix: 1.65 (0.23), residues: 602 sheet: -0.73 (0.30), residues: 290 loop : -2.66 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 308 PHE 0.054 0.001 PHE 7 332 TYR 0.012 0.001 TYR 7 355 ARG 0.002 0.000 ARG h 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.98 seconds wall clock time: 46 minutes 0.12 seconds (2760.12 seconds total)