Starting phenix.real_space_refine on Tue Jul 23 18:08:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4b_41877/07_2024/8u4b_41877_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12534 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 8388 2.51 5 N 2284 2.21 5 O 2444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13212 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6606 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 774} Chain breaks: 5 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6606 Classifications: {'peptide': 817} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 774} Chain breaks: 5 Time building chain proxies: 6.87, per 1000 atoms: 0.52 Number of scatterers: 13212 At special positions: 0 Unit cell: (89.64, 147.96, 141.48, 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 96 16.00 O 2444 8.00 N 2284 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.67 Conformation dependent library (CDL) restraints added in 2.3 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3084 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 28 sheets defined 14.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.681A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.894A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 47' Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.379A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.954A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.620A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.777A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 4.036A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.053A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'A' and resid 875 through 882 Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.683A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.895A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 47' Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 139 through 143 removed outlier: 4.385A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.955A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.136A pdb=" N ASN B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.777A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.053A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 639 through 644 removed outlier: 4.111A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'B' and resid 874 through 882 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.494A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR A 91 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ARG A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 146 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 321 removed outlier: 10.304A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 10.304A pdb=" N VAL A 335 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N LEU A 315 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ASN A 337 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY A 317 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.588A pdb=" N TYR A 477 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 485 " --> pdb=" O MET A 553 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 Processing sheet with id=AB2, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.876A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 611 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.611A pdb=" N GLU A 772 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 630 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 790 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 831 through 834 removed outlier: 3.639A pdb=" N CYS A 884 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 868 through 874 removed outlier: 3.838A pdb=" N LEU A 856 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 896 " --> pdb=" O THR A 913 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 913 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.497A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 146 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC1, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 321 removed outlier: 10.307A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 321 removed outlier: 10.307A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.596A pdb=" N TYR B 477 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 485 " --> pdb=" O MET B 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AC7, first strand: chain 'B' and resid 599 through 605 removed outlier: 5.876A pdb=" N ASP B 600 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 616 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 611 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 771 through 772 removed outlier: 3.545A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 790 " --> pdb=" O GLN B 635 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 831 through 834 removed outlier: 3.654A pdb=" N CYS B 884 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 868 through 873 removed outlier: 3.838A pdb=" N LEU B 856 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 896 " --> pdb=" O THR B 913 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 913 " --> pdb=" O VAL B 896 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 840 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: 4.50 Time building geometry restraints manager: 5.16 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: 4336 1.34 - 1.46: 2980 1.46 - 1.58: 6100 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 13534 Sorted by residual: bond pdb=" CA GLN A 465 " pdb=" C GLN A 465 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.56e-02 4.11e+03 3.42e+00 bond pdb=" C PRO A 307 " pdb=" N CYS A 308 " ideal model delta sigma weight residual 1.329 1.314 0.015 1.35e-02 5.49e+03 1.28e+00 bond pdb=" C PRO B 307 " pdb=" N CYS B 308 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.59e-02 3.96e+03 1.20e+00 bond pdb=" CB MET B 294 " pdb=" CG MET B 294 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.92e-01 bond pdb=" CB GLN B 272 " pdb=" CG GLN B 272 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.81e-01 ... (remaining 13529 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 381 106.31 - 113.25: 7206 113.25 - 120.19: 4705 120.19 - 127.12: 5872 127.12 - 134.06: 180 Bond angle restraints: 18344 Sorted by residual: angle pdb=" CB MET B 294 " pdb=" CG MET B 294 " pdb=" SD MET B 294 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " ideal model delta sigma weight residual 112.70 122.55 -9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA MET B 294 " pdb=" CB MET B 294 " pdb=" CG MET B 294 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.18e+00 angle pdb=" CA MET A 294 " pdb=" CB MET A 294 " pdb=" CG MET A 294 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.39e+00 angle pdb=" CA GLU A 30 " pdb=" CB GLU A 30 " pdb=" CG GLU A 30 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.27e+00 ... (remaining 18339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7028 17.51 - 35.01: 919 35.01 - 52.52: 218 52.52 - 70.02: 36 70.02 - 87.53: 13 Dihedral angle restraints: 8214 sinusoidal: 3438 harmonic: 4776 Sorted by residual: dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual -86.00 -156.17 70.17 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS B 259 " pdb=" SG CYS B 259 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual -86.00 -155.19 69.19 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS B 304 " pdb=" SG CYS B 304 " pdb=" SG CYS B 308 " pdb=" CB CYS B 308 " ideal model delta sinusoidal sigma weight residual -86.00 -28.86 -57.14 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 8211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1133 0.027 - 0.054: 487 0.054 - 0.080: 180 0.080 - 0.107: 125 0.107 - 0.134: 69 Chirality restraints: 1994 Sorted by residual: chirality pdb=" CA THR A 802 " pdb=" N THR A 802 " pdb=" C THR A 802 " pdb=" CB THR A 802 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 285 " pdb=" N ILE A 285 " pdb=" C ILE A 285 " pdb=" CB ILE A 285 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA THR B 802 " pdb=" N THR B 802 " pdb=" C THR B 802 " pdb=" CB THR B 802 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1991 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 285 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 286 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 285 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 286 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 306 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 307 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.022 5.00e-02 4.00e+02 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 396 2.70 - 3.25: 13126 3.25 - 3.80: 21020 3.80 - 4.35: 26581 4.35 - 4.90: 43111 Nonbonded interactions: 104234 Sorted by model distance: nonbonded pdb=" OG SER B 399 " pdb=" O GLN B 423 " model vdw 2.146 2.440 nonbonded pdb=" OH TYR A 127 " pdb=" O ILE A 158 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR B 127 " pdb=" O ILE B 158 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR A 374 " pdb=" OH TYR B 374 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN A 295 " pdb=" OG SER A 297 " model vdw 2.234 2.440 ... (remaining 104229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 1.120 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13534 Z= 0.195 Angle : 0.594 11.416 18344 Z= 0.305 Chirality : 0.044 0.134 1994 Planarity : 0.003 0.045 2368 Dihedral : 16.017 87.531 5028 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 0.07 % Allowed : 24.43 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1610 helix: 0.35 (0.45), residues: 158 sheet: -0.23 (0.28), residues: 346 loop : -0.94 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 414 HIS 0.007 0.001 HIS B 264 PHE 0.013 0.001 PHE A 705 TYR 0.011 0.001 TYR B 864 ARG 0.006 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7348 (mmt) cc_final: 0.6964 (mmt) REVERT: A 703 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8845 (tppp) REVERT: B 38 MET cc_start: 0.7412 (mmt) cc_final: 0.7036 (mmt) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.2289 time to fit residues: 13.6209 Evaluate side-chains 31 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 703 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13534 Z= 0.190 Angle : 0.557 7.860 18344 Z= 0.286 Chirality : 0.044 0.155 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.382 49.374 1794 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 1.41 % Allowed : 24.02 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1610 helix: 0.83 (0.46), residues: 158 sheet: -0.21 (0.27), residues: 380 loop : -0.98 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.005 0.001 HIS B 264 PHE 0.013 0.001 PHE A 631 TYR 0.009 0.001 TYR A 507 ARG 0.005 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 31 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7529 (mmt) cc_final: 0.6825 (mmt) REVERT: A 121 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (mppt) REVERT: A 553 MET cc_start: 0.8312 (mmm) cc_final: 0.7737 (mtt) REVERT: B 38 MET cc_start: 0.7577 (mmt) cc_final: 0.6873 (mmt) REVERT: B 121 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8570 (mppt) REVERT: B 553 MET cc_start: 0.8257 (mmm) cc_final: 0.7677 (mtt) outliers start: 21 outliers final: 3 residues processed: 52 average time/residue: 0.2052 time to fit residues: 18.3571 Evaluate side-chains 35 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 798 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS B 263 HIS ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 13534 Z= 0.470 Angle : 0.683 11.650 18344 Z= 0.349 Chirality : 0.047 0.187 1994 Planarity : 0.004 0.042 2368 Dihedral : 4.794 28.082 1790 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.26 % Favored : 91.61 % Rotamer: Outliers : 4.37 % Allowed : 21.60 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.14 (0.22), residues: 1610 helix: 0.54 (0.44), residues: 158 sheet: -0.43 (0.27), residues: 376 loop : -1.11 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 414 HIS 0.005 0.001 HIS B 440 PHE 0.021 0.002 PHE B 705 TYR 0.014 0.001 TYR A 857 ARG 0.007 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 34 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7795 (mmt) cc_final: 0.7336 (mmt) REVERT: A 166 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5678 (tptt) REVERT: A 882 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8373 (tpm170) REVERT: B 38 MET cc_start: 0.7828 (mmt) cc_final: 0.7312 (mmt) REVERT: B 121 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8640 (mppt) REVERT: B 166 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5623 (tptt) REVERT: B 882 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8412 (tpm170) outliers start: 65 outliers final: 29 residues processed: 95 average time/residue: 0.2220 time to fit residues: 33.0688 Evaluate side-chains 65 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 31 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 247 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 914 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 914 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 HIS B 610 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13534 Z= 0.170 Angle : 0.569 11.627 18344 Z= 0.284 Chirality : 0.044 0.191 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.494 23.008 1790 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.09 % Allowed : 24.36 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.03 (0.22), residues: 1610 helix: 0.59 (0.44), residues: 158 sheet: -0.31 (0.27), residues: 376 loop : -1.06 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 414 HIS 0.004 0.001 HIS B 264 PHE 0.013 0.001 PHE B 705 TYR 0.012 0.001 TYR A 507 ARG 0.006 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 36 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7844 (mmt) cc_final: 0.7319 (mmt) REVERT: A 435 CYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 38 MET cc_start: 0.7859 (mmt) cc_final: 0.7304 (mmt) REVERT: B 121 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (mppt) outliers start: 31 outliers final: 10 residues processed: 67 average time/residue: 0.1871 time to fit residues: 21.8027 Evaluate side-chains 44 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 886 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13534 Z= 0.215 Angle : 0.550 9.120 18344 Z= 0.278 Chirality : 0.044 0.146 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.419 22.387 1790 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 2.49 % Allowed : 23.82 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.01 (0.22), residues: 1610 helix: 0.51 (0.44), residues: 158 sheet: -0.25 (0.27), residues: 376 loop : -1.04 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 414 HIS 0.003 0.001 HIS B 841 PHE 0.014 0.001 PHE B 705 TYR 0.009 0.001 TYR B 857 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 33 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7858 (mmt) cc_final: 0.7318 (mmt) REVERT: A 435 CYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8248 (p) REVERT: A 553 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: B 38 MET cc_start: 0.7877 (mmt) cc_final: 0.7298 (mmt) REVERT: B 121 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8537 (mppt) REVERT: B 553 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7902 (mmm) outliers start: 37 outliers final: 17 residues processed: 68 average time/residue: 0.1964 time to fit residues: 22.5340 Evaluate side-chains 50 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 29 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.0870 chunk 141 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13534 Z= 0.231 Angle : 0.556 9.950 18344 Z= 0.281 Chirality : 0.044 0.147 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.463 30.669 1790 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 3.10 % Allowed : 22.88 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1610 helix: 0.47 (0.44), residues: 158 sheet: -0.23 (0.27), residues: 376 loop : -1.02 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.003 0.001 HIS A 187 PHE 0.015 0.001 PHE B 705 TYR 0.010 0.001 TYR A 857 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 29 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7905 (mmt) cc_final: 0.7325 (mmt) REVERT: A 61 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8511 (tt) REVERT: A 435 CYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8282 (p) REVERT: A 442 MET cc_start: 0.8633 (mmp) cc_final: 0.8188 (mmp) REVERT: A 553 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7948 (mmm) REVERT: A 882 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8225 (tpm170) REVERT: B 38 MET cc_start: 0.7913 (mmt) cc_final: 0.7347 (mmt) REVERT: B 121 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (mppt) REVERT: B 435 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 553 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: B 882 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8325 (tpm170) outliers start: 46 outliers final: 27 residues processed: 73 average time/residue: 0.2205 time to fit residues: 26.1686 Evaluate side-chains 65 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 30 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 435 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 882 ARG Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 131 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13534 Z= 0.182 Angle : 0.540 10.672 18344 Z= 0.270 Chirality : 0.044 0.138 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.339 28.507 1790 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.56 % Allowed : 23.49 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1610 helix: 0.51 (0.44), residues: 158 sheet: -0.23 (0.27), residues: 366 loop : -0.98 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 414 HIS 0.003 0.001 HIS B 841 PHE 0.012 0.001 PHE B 705 TYR 0.010 0.001 TYR A 507 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 33 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7847 (mmt) cc_final: 0.7259 (mmt) REVERT: A 442 MET cc_start: 0.8671 (mmp) cc_final: 0.8329 (mmp) REVERT: A 553 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7992 (mmm) REVERT: B 38 MET cc_start: 0.7852 (mmt) cc_final: 0.7233 (mmt) REVERT: B 121 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (mppt) REVERT: B 435 CYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (p) REVERT: B 553 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7915 (mmm) outliers start: 38 outliers final: 23 residues processed: 69 average time/residue: 0.1830 time to fit residues: 21.7526 Evaluate side-chains 57 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 30 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 435 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13534 Z= 0.153 Angle : 0.531 11.152 18344 Z= 0.264 Chirality : 0.044 0.140 1994 Planarity : 0.003 0.044 2368 Dihedral : 4.211 25.888 1790 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.15 % Favored : 93.73 % Rotamer: Outliers : 2.56 % Allowed : 23.28 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1610 helix: 0.45 (0.44), residues: 158 sheet: -0.22 (0.27), residues: 362 loop : -0.95 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.004 0.000 HIS A 440 PHE 0.010 0.001 PHE B 701 TYR 0.011 0.001 TYR A 507 ARG 0.004 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 30 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7761 (mmt) cc_final: 0.7140 (mmt) REVERT: A 435 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 553 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: B 38 MET cc_start: 0.7774 (mmt) cc_final: 0.7152 (mmt) REVERT: B 121 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8435 (mppt) REVERT: B 435 CYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8415 (p) REVERT: B 553 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7866 (mmm) outliers start: 38 outliers final: 23 residues processed: 66 average time/residue: 0.1964 time to fit residues: 22.0800 Evaluate side-chains 58 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 30 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 0.0970 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13534 Z= 0.171 Angle : 0.552 11.089 18344 Z= 0.271 Chirality : 0.044 0.164 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.221 29.574 1790 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.48 % Rotamer: Outliers : 2.15 % Allowed : 23.55 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1610 helix: 0.52 (0.44), residues: 158 sheet: -0.17 (0.27), residues: 362 loop : -0.91 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.002 0.000 HIS B 841 PHE 0.011 0.001 PHE B 701 TYR 0.010 0.001 TYR A 507 ARG 0.004 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 31 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7728 (mmt) cc_final: 0.7106 (mmt) REVERT: A 553 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7910 (mmm) REVERT: B 38 MET cc_start: 0.7770 (mmt) cc_final: 0.7148 (mmt) REVERT: B 121 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8451 (mppt) REVERT: B 553 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7874 (mmm) outliers start: 32 outliers final: 24 residues processed: 61 average time/residue: 0.1901 time to fit residues: 20.3179 Evaluate side-chains 57 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 30 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13534 Z= 0.188 Angle : 0.557 11.431 18344 Z= 0.273 Chirality : 0.044 0.155 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.226 28.619 1790 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 2.15 % Allowed : 23.42 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1610 helix: 0.51 (0.44), residues: 158 sheet: -0.16 (0.27), residues: 362 loop : -0.90 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 414 HIS 0.004 0.001 HIS B 187 PHE 0.012 0.001 PHE B 705 TYR 0.009 0.001 TYR A 507 ARG 0.004 0.000 ARG B 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 33 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7761 (mmt) cc_final: 0.7151 (mmt) REVERT: A 553 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7930 (mmm) REVERT: B 38 MET cc_start: 0.7794 (mmt) cc_final: 0.7173 (mmt) REVERT: B 121 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8455 (mppt) REVERT: B 553 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7892 (mmm) outliers start: 32 outliers final: 25 residues processed: 63 average time/residue: 0.1949 time to fit residues: 21.6078 Evaluate side-chains 58 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 30 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 884 CYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 884 CYS Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 896 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 53 optimal weight: 0.0010 chunk 132 optimal weight: 0.0050 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 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 = 0.3606 r_free = 0.3606 target = 0.074049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055094 restraints weight = 50570.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.056829 restraints weight = 30762.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058037 restraints weight = 22614.050| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13534 Z= 0.154 Angle : 0.568 11.844 18344 Z= 0.274 Chirality : 0.044 0.161 1994 Planarity : 0.003 0.043 2368 Dihedral : 4.138 26.677 1790 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 1.75 % Allowed : 24.02 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1610 helix: 0.79 (0.46), residues: 146 sheet: -0.09 (0.27), residues: 362 loop : -0.84 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 414 HIS 0.010 0.001 HIS B 187 PHE 0.011 0.001 PHE B 701 TYR 0.011 0.001 TYR A 507 ARG 0.004 0.000 ARG B 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.60 seconds wall clock time: 41 minutes 12.08 seconds (2472.08 seconds total)