Starting phenix.real_space_refine on Tue Dec 31 00:12:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.map" model { file = "/net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guy_34281/12_2024/8guy_34281.cif" } resolution = 4.18 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= 0.048 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 114 5.16 5 C 9006 2.51 5 N 2456 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14222 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "F" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 residue: pdb=" N ATYR D 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 26 " occ=0.50 Time building chain proxies: 14.93, per 1000 atoms: 1.05 Number of scatterers: 14222 At special positions: 0 Unit cell: (119.84, 132.68, 174.41, 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 114 16.00 O 2646 8.00 N 2456 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 683 " - pdb=" SG CYS F 683 " distance=2.04 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.02 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.02 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.04 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.02 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.19 Conformation dependent library (CDL) restraints added in 3.4 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 32 sheets defined 15.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.923A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.096A pdb=" N ILE E 131 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.034A pdb=" N ILE E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.534A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 413 through 417 removed outlier: 3.526A pdb=" N HIS E 417 " --> pdb=" O TRP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 444 removed outlier: 3.851A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 644 removed outlier: 3.592A pdb=" N PHE E 642 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 643 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 644 " --> pdb=" O LEU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 714 removed outlier: 3.675A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 712 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 714 " --> pdb=" O HIS E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 813 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.532A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.070A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.531A pdb=" N GLU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 removed outlier: 4.165A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.021A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.509A pdb=" N ASN F 152 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.510A pdb=" N HIS F 417 " --> pdb=" O TRP F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.877A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 644 removed outlier: 3.530A pdb=" N PHE F 642 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 644 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 714 removed outlier: 3.642A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 708 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 711 " --> pdb=" O ASP F 707 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 712 " --> pdb=" O TYR F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU E 6 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE E 29 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS E 8 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.832A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU E 36 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE E 13 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET E 38 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 64 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.362A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312 removed outlier: 3.856A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321 removed outlier: 3.884A pdb=" N LYS E 319 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.678A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 599 through 605 removed outlier: 5.491A pdb=" N ASP E 600 " --> pdb=" O LYS E 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 616 " --> pdb=" O ASP E 600 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 612 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 611 " --> pdb=" O ILE E 770 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 4.124A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 819 through 822 removed outlier: 3.543A pdb=" N VAL E 828 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 886 " --> pdb=" O TRP E 897 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP E 897 " --> pdb=" O ILE E 886 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA E 888 " --> pdb=" O GLY E 895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU F 6 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE F 29 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS F 8 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 14 removed outlier: 3.658A pdb=" N PHE F 64 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 37 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.237A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC3, first strand: chain 'F' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.801A pdb=" N ILE F 364 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 318 through 321 removed outlier: 3.777A pdb=" N LYS F 319 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE F 341 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AC9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.530A pdb=" N LYS F 508 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 564 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 599 through 605 removed outlier: 5.430A pdb=" N ASP F 600 " --> pdb=" O LYS F 616 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS F 616 " --> pdb=" O ASP F 600 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 612 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 611 " --> pdb=" O ILE F 770 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 761 through 762 removed outlier: 3.680A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 819 through 822 removed outlier: 3.545A pdb=" N VAL F 828 " --> pdb=" O LEU F 874 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 886 " --> pdb=" O TRP F 897 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP F 897 " --> pdb=" O ILE F 886 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA F 888 " --> pdb=" O GLY F 895 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 789 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: 6.05 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4683 1.35 - 1.48: 3636 1.48 - 1.60: 6121 1.60 - 1.73: 0 1.73 - 1.85: 136 Bond restraints: 14576 Sorted by residual: bond pdb=" CB GLU F 637 " pdb=" CG GLU F 637 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB CYS F 435 " pdb=" SG CYS F 435 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB GLU E 637 " pdb=" CG GLU E 637 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB CYS E 435 " pdb=" SG CYS E 435 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CA THR E 578 " pdb=" CB THR E 578 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.61e-02 3.86e+03 2.51e+00 ... (remaining 14571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18992 2.32 - 4.63: 652 4.63 - 6.95: 97 6.95 - 9.27: 23 9.27 - 11.59: 6 Bond angle restraints: 19770 Sorted by residual: angle pdb=" N VAL E 445 " pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 112.96 105.76 7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" C ARG E 577 " pdb=" N THR E 578 " pdb=" CA THR E 578 " ideal model delta sigma weight residual 122.82 128.40 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ARG F 14 " pdb=" N ASN F 15 " pdb=" CA ASN F 15 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLU E 808 " pdb=" CA GLU E 808 " pdb=" C GLU E 808 " ideal model delta sigma weight residual 110.53 115.59 -5.06 1.32e+00 5.74e-01 1.47e+01 angle pdb=" CA CYS F 308 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 19765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7845 17.90 - 35.80: 830 35.80 - 53.70: 130 53.70 - 71.60: 47 71.60 - 89.51: 16 Dihedral angle restraints: 8868 sinusoidal: 3704 harmonic: 5164 Sorted by residual: dihedral pdb=" CA PRO E 243 " pdb=" C PRO E 243 " pdb=" N PRO E 244 " pdb=" CA PRO E 244 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 dihedral pdb=" CB CYS F 647 " pdb=" SG CYS F 647 " pdb=" SG CYS F 860 " pdb=" CB CYS F 860 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA PRO F 243 " pdb=" C PRO F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 134.03 45.97 0 5.00e+00 4.00e-02 8.45e+01 ... (remaining 8865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1654 0.065 - 0.131: 403 0.131 - 0.196: 67 0.196 - 0.262: 15 0.262 - 0.327: 1 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CB THR F 790 " pdb=" CA THR F 790 " pdb=" OG1 THR F 790 " pdb=" CG2 THR F 790 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR F 790 " pdb=" N THR F 790 " pdb=" C THR F 790 " pdb=" CB THR F 790 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE E 781 " pdb=" CA ILE E 781 " pdb=" CG1 ILE E 781 " pdb=" CG2 ILE E 781 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2137 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 243 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO F 244 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 244 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 244 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 242 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO F 243 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " 0.047 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2977 2.78 - 3.31: 12547 3.31 - 3.84: 23562 3.84 - 4.37: 25822 4.37 - 4.90: 43345 Nonbonded interactions: 108253 Sorted by model distance: nonbonded pdb=" OD1 ASP E 59 " pdb=" OG SER E 85 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP F 59 " pdb=" OG SER F 85 " model vdw 2.258 3.040 nonbonded pdb=" OG SER E 116 " pdb=" OD1 ASN E 143 " model vdw 2.299 3.040 nonbonded pdb=" OG SER F 116 " pdb=" OD1 ASN F 143 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR F 334 " pdb=" OE1 GLU F 362 " model vdw 2.333 3.040 ... (remaining 108248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 3 through 25 or resid 27)) selection = (chain 'D' and (resid 3 through 25 or resid 27)) } ncs_group { reference = (chain 'E' and (resid 1 through 143 or resid 145 through 907)) selection = (chain 'F' and (resid 1 through 143 or resid 145 through 907)) } 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=0.50 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: 2.780 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 42.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14576 Z= 0.336 Angle : 1.005 11.587 19770 Z= 0.539 Chirality : 0.060 0.327 2140 Planarity : 0.007 0.112 2566 Dihedral : 14.547 89.506 5408 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.12 % 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: -4.23 (0.17), residues: 1744 helix: -4.43 (0.16), residues: 216 sheet: -1.99 (0.27), residues: 316 loop : -2.92 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 412 HIS 0.007 0.001 HIS F 275 PHE 0.021 0.002 PHE E 776 TYR 0.018 0.002 TYR F 708 ARG 0.013 0.001 ARG E 774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8459 (tp) cc_final: 0.8086 (tp) REVERT: E 405 ASN cc_start: 0.8688 (m-40) cc_final: 0.8431 (m110) REVERT: E 439 ILE cc_start: 0.9224 (pt) cc_final: 0.8977 (mt) REVERT: E 442 MET cc_start: 0.9351 (tpt) cc_final: 0.8902 (tpt) REVERT: E 698 GLU cc_start: 0.7758 (pp20) cc_final: 0.7524 (tm-30) REVERT: A 2 ILE cc_start: 0.9529 (tt) cc_final: 0.9317 (tt) REVERT: C 17 GLU cc_start: 0.8504 (pp20) cc_final: 0.8073 (pp20) REVERT: F 439 ILE cc_start: 0.8987 (pt) cc_final: 0.8698 (mt) REVERT: F 442 MET cc_start: 0.9295 (tpt) cc_final: 0.9005 (tpt) REVERT: F 698 GLU cc_start: 0.8177 (pp20) cc_final: 0.7891 (tm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2352 time to fit residues: 49.8644 Evaluate side-chains 79 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN E 249 GLN E 282 ASN E 589 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 32 HIS F 177 GLN F 249 GLN F 431 ASN F 589 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14576 Z= 0.226 Angle : 0.700 6.720 19770 Z= 0.369 Chirality : 0.047 0.194 2140 Planarity : 0.006 0.100 2566 Dihedral : 6.559 76.263 1938 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.25 % Allowed : 3.30 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.18), residues: 1744 helix: -3.21 (0.26), residues: 190 sheet: -1.89 (0.27), residues: 326 loop : -2.41 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 412 HIS 0.007 0.001 HIS E 858 PHE 0.018 0.002 PHE E 497 TYR 0.013 0.001 TYR E 708 ARG 0.005 0.001 ARG F 717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8090 (tp) cc_final: 0.7228 (tp) REVERT: E 57 ILE cc_start: 0.9008 (mt) cc_final: 0.8649 (mt) REVERT: E 442 MET cc_start: 0.9159 (tpt) cc_final: 0.8747 (tpt) REVERT: E 572 PHE cc_start: 0.7712 (t80) cc_final: 0.7475 (t80) REVERT: E 613 LEU cc_start: 0.8640 (tp) cc_final: 0.8437 (pp) REVERT: D 6 LEU cc_start: 0.9203 (mt) cc_final: 0.8985 (mt) REVERT: F 442 MET cc_start: 0.9093 (tpt) cc_final: 0.8882 (tpt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2176 time to fit residues: 39.8569 Evaluate side-chains 67 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 107 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 chunk 171 optimal weight: 50.0000 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS F 187 HIS F 431 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14576 Z= 0.201 Angle : 0.655 8.582 19770 Z= 0.341 Chirality : 0.046 0.189 2140 Planarity : 0.005 0.103 2566 Dihedral : 6.159 83.547 1938 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.25 % Allowed : 2.43 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.19), residues: 1744 helix: -2.40 (0.31), residues: 196 sheet: -1.77 (0.26), residues: 364 loop : -2.20 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 412 HIS 0.003 0.000 HIS F 429 PHE 0.023 0.002 PHE F 427 TYR 0.013 0.001 TYR E 401 ARG 0.005 0.000 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8100 (tp) cc_final: 0.7419 (tp) REVERT: E 405 ASN cc_start: 0.8806 (m-40) cc_final: 0.8531 (m-40) REVERT: E 504 MET cc_start: 0.8140 (mtp) cc_final: 0.7860 (mtp) REVERT: F 36 LEU cc_start: 0.8437 (tp) cc_final: 0.8133 (tp) REVERT: F 333 CYS cc_start: 0.6291 (p) cc_final: 0.6033 (p) REVERT: F 614 LYS cc_start: 0.9258 (ptpp) cc_final: 0.9055 (ptmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2375 time to fit residues: 39.5177 Evaluate side-chains 69 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14576 Z= 0.256 Angle : 0.656 7.243 19770 Z= 0.339 Chirality : 0.047 0.187 2140 Planarity : 0.005 0.105 2566 Dihedral : 6.069 82.884 1938 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.25 % Allowed : 2.43 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.86 (0.19), residues: 1744 helix: -1.63 (0.35), residues: 194 sheet: -1.63 (0.26), residues: 350 loop : -2.15 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 529 HIS 0.004 0.001 HIS E 429 PHE 0.025 0.002 PHE E 572 TYR 0.013 0.001 TYR E 60 ARG 0.003 0.000 ARG F 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8199 (tp) cc_final: 0.7485 (tp) REVERT: E 405 ASN cc_start: 0.8893 (m-40) cc_final: 0.8574 (m110) REVERT: E 442 MET cc_start: 0.9302 (tpt) cc_final: 0.8801 (tpt) REVERT: E 504 MET cc_start: 0.8191 (mtp) cc_final: 0.7967 (mtm) REVERT: A 14 TYR cc_start: 0.7790 (t80) cc_final: 0.7180 (t80) REVERT: A 17 GLU cc_start: 0.8357 (pp20) cc_final: 0.8111 (pp20) REVERT: F 36 LEU cc_start: 0.8297 (tp) cc_final: 0.8074 (tp) REVERT: F 56 MET cc_start: 0.7030 (ttt) cc_final: 0.6709 (ttt) REVERT: F 333 CYS cc_start: 0.6152 (p) cc_final: 0.5951 (p) REVERT: F 442 MET cc_start: 0.9146 (tpt) cc_final: 0.8920 (tpt) REVERT: F 504 MET cc_start: 0.8200 (mtp) cc_final: 0.7948 (mtm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2605 time to fit residues: 35.1148 Evaluate side-chains 59 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 HIS ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 423 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14576 Z= 0.232 Angle : 0.635 6.663 19770 Z= 0.328 Chirality : 0.046 0.187 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.866 82.078 1938 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.25 % Allowed : 1.62 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.70 (0.20), residues: 1744 helix: -1.33 (0.37), residues: 194 sheet: -1.48 (0.27), residues: 340 loop : -2.09 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 412 HIS 0.003 0.001 HIS D 5 PHE 0.022 0.002 PHE F 382 TYR 0.012 0.001 TYR E 401 ARG 0.006 0.000 ARG F 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8054 (tp) cc_final: 0.7292 (tp) REVERT: E 333 CYS cc_start: 0.6688 (p) cc_final: 0.6444 (p) REVERT: E 405 ASN cc_start: 0.8897 (m-40) cc_final: 0.8554 (m110) REVERT: E 504 MET cc_start: 0.8221 (mtp) cc_final: 0.7970 (mtm) REVERT: A 14 TYR cc_start: 0.7727 (t80) cc_final: 0.7032 (t80) REVERT: A 17 GLU cc_start: 0.8321 (pp20) cc_final: 0.8026 (pp20) REVERT: F 56 MET cc_start: 0.6892 (ttt) cc_final: 0.6554 (ttt) REVERT: F 333 CYS cc_start: 0.6578 (p) cc_final: 0.6338 (p) REVERT: F 504 MET cc_start: 0.8225 (mtp) cc_final: 0.7924 (mtm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2249 time to fit residues: 32.2676 Evaluate side-chains 59 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14576 Z= 0.163 Angle : 0.606 6.930 19770 Z= 0.311 Chirality : 0.045 0.185 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.612 81.098 1938 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.25 % Allowed : 1.06 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.48 (0.20), residues: 1744 helix: -1.32 (0.37), residues: 194 sheet: -1.26 (0.28), residues: 350 loop : -1.93 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 529 HIS 0.003 0.000 HIS F 829 PHE 0.016 0.001 PHE F 565 TYR 0.015 0.001 TYR C 14 ARG 0.003 0.000 ARG E 702 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8006 (tp) cc_final: 0.7275 (tp) REVERT: E 262 LEU cc_start: 0.9174 (mt) cc_final: 0.8968 (mt) REVERT: E 294 MET cc_start: 0.8292 (ppp) cc_final: 0.7893 (tpp) REVERT: E 333 CYS cc_start: 0.6659 (p) cc_final: 0.6371 (p) REVERT: E 405 ASN cc_start: 0.8820 (m-40) cc_final: 0.8400 (m110) REVERT: E 442 MET cc_start: 0.9245 (tpt) cc_final: 0.8898 (tpt) REVERT: E 504 MET cc_start: 0.8200 (mtp) cc_final: 0.7908 (mtm) REVERT: E 553 MET cc_start: 0.8647 (mtp) cc_final: 0.7898 (mtt) REVERT: A 17 GLU cc_start: 0.8288 (pp20) cc_final: 0.8066 (mp0) REVERT: B 6 LEU cc_start: 0.9153 (mt) cc_final: 0.8897 (mt) REVERT: C 14 TYR cc_start: 0.7797 (t80) cc_final: 0.7071 (t80) REVERT: F 56 MET cc_start: 0.6983 (ttt) cc_final: 0.6731 (ttt) REVERT: F 333 CYS cc_start: 0.6514 (p) cc_final: 0.6262 (p) REVERT: F 504 MET cc_start: 0.8158 (mtp) cc_final: 0.7857 (mtm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2195 time to fit residues: 32.7341 Evaluate side-chains 64 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 ASN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14576 Z= 0.336 Angle : 0.688 7.846 19770 Z= 0.353 Chirality : 0.047 0.176 2140 Planarity : 0.005 0.106 2566 Dihedral : 5.846 77.987 1938 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.25 % Allowed : 0.93 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.52 (0.20), residues: 1744 helix: -0.75 (0.41), residues: 170 sheet: -1.32 (0.28), residues: 330 loop : -2.04 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 832 HIS 0.005 0.001 HIS F 263 PHE 0.015 0.002 PHE F 565 TYR 0.016 0.001 TYR F 60 ARG 0.012 0.001 ARG F 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8039 (tp) cc_final: 0.7307 (tp) REVERT: E 333 CYS cc_start: 0.6890 (p) cc_final: 0.6629 (p) REVERT: E 405 ASN cc_start: 0.8941 (m-40) cc_final: 0.8616 (m110) REVERT: E 442 MET cc_start: 0.9258 (tpt) cc_final: 0.8664 (tpt) REVERT: E 504 MET cc_start: 0.8197 (mtp) cc_final: 0.7985 (mtm) REVERT: A 17 GLU cc_start: 0.8432 (pp20) cc_final: 0.8178 (mp0) REVERT: C 14 TYR cc_start: 0.7917 (t80) cc_final: 0.7457 (t80) REVERT: C 17 GLU cc_start: 0.8580 (pp20) cc_final: 0.8317 (pp20) REVERT: F 256 PHE cc_start: 0.9404 (p90) cc_final: 0.9184 (p90) REVERT: F 333 CYS cc_start: 0.6801 (p) cc_final: 0.6590 (p) REVERT: F 442 MET cc_start: 0.9281 (tpt) cc_final: 0.8924 (tpt) REVERT: F 504 MET cc_start: 0.8186 (mtp) cc_final: 0.7941 (mtm) REVERT: F 602 ILE cc_start: 0.9136 (mm) cc_final: 0.8833 (mm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2168 time to fit residues: 27.7579 Evaluate side-chains 55 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 547 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 HIS ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14576 Z= 0.211 Angle : 0.620 7.219 19770 Z= 0.317 Chirality : 0.046 0.173 2140 Planarity : 0.005 0.109 2566 Dihedral : 5.628 78.303 1938 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.25 % Allowed : 0.62 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.38 (0.20), residues: 1744 helix: -0.89 (0.40), residues: 182 sheet: -1.21 (0.28), residues: 330 loop : -1.91 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 412 HIS 0.003 0.001 HIS E 417 PHE 0.013 0.001 PHE D 24 TYR 0.011 0.001 TYR E 60 ARG 0.004 0.000 ARG E 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7897 (tp) cc_final: 0.7086 (tp) REVERT: E 262 LEU cc_start: 0.9194 (mt) cc_final: 0.8993 (mt) REVERT: E 294 MET cc_start: 0.8330 (ppp) cc_final: 0.7855 (tpp) REVERT: E 333 CYS cc_start: 0.6903 (p) cc_final: 0.6596 (p) REVERT: E 405 ASN cc_start: 0.8870 (m-40) cc_final: 0.8512 (m110) REVERT: E 504 MET cc_start: 0.8209 (mtp) cc_final: 0.7976 (mtm) REVERT: E 553 MET cc_start: 0.8755 (mtp) cc_final: 0.8161 (mtt) REVERT: A 17 GLU cc_start: 0.8356 (pp20) cc_final: 0.8116 (pp20) REVERT: B 6 LEU cc_start: 0.9150 (mt) cc_final: 0.8915 (mt) REVERT: C 14 TYR cc_start: 0.7979 (t80) cc_final: 0.7534 (t80) REVERT: C 17 GLU cc_start: 0.8530 (pp20) cc_final: 0.8293 (pp20) REVERT: F 56 MET cc_start: 0.6882 (ttt) cc_final: 0.6555 (ttt) REVERT: F 256 PHE cc_start: 0.9385 (p90) cc_final: 0.9174 (p90) REVERT: F 333 CYS cc_start: 0.6650 (p) cc_final: 0.6395 (p) REVERT: F 442 MET cc_start: 0.9322 (tpt) cc_final: 0.8969 (tpt) REVERT: F 504 MET cc_start: 0.8233 (mtp) cc_final: 0.7961 (mtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2139 time to fit residues: 28.1958 Evaluate side-chains 59 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0970 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 165 optimal weight: 40.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 HIS ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14576 Z= 0.258 Angle : 0.647 7.402 19770 Z= 0.330 Chirality : 0.046 0.170 2140 Planarity : 0.005 0.107 2566 Dihedral : 5.678 75.559 1938 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.25 % Allowed : 0.31 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.45 (0.20), residues: 1744 helix: -0.90 (0.39), residues: 182 sheet: -1.38 (0.29), residues: 314 loop : -1.93 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 832 HIS 0.003 0.001 HIS F 199 PHE 0.020 0.002 PHE E 497 TYR 0.014 0.001 TYR E 60 ARG 0.005 0.000 ARG F 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7974 (tp) cc_final: 0.7164 (tp) REVERT: E 333 CYS cc_start: 0.6858 (p) cc_final: 0.6595 (p) REVERT: E 405 ASN cc_start: 0.8912 (m-40) cc_final: 0.8591 (m110) REVERT: E 442 MET cc_start: 0.9289 (tpt) cc_final: 0.8920 (tpt) REVERT: E 504 MET cc_start: 0.8217 (mtp) cc_final: 0.7907 (mtm) REVERT: A 14 TYR cc_start: 0.7736 (t80) cc_final: 0.7398 (t80) REVERT: A 17 GLU cc_start: 0.8355 (pp20) cc_final: 0.8062 (pp20) REVERT: F 56 MET cc_start: 0.6823 (ttt) cc_final: 0.6447 (ttt) REVERT: F 256 PHE cc_start: 0.9382 (p90) cc_final: 0.9143 (p90) REVERT: F 333 CYS cc_start: 0.6797 (p) cc_final: 0.6512 (p) REVERT: F 442 MET cc_start: 0.9309 (tpt) cc_final: 0.8955 (tpt) REVERT: F 504 MET cc_start: 0.8156 (mtp) cc_final: 0.7894 (mtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2009 time to fit residues: 26.6193 Evaluate side-chains 61 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 173 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14576 Z= 0.176 Angle : 0.605 7.487 19770 Z= 0.308 Chirality : 0.045 0.172 2140 Planarity : 0.005 0.110 2566 Dihedral : 5.501 76.553 1938 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.25 % Allowed : 0.19 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.29 (0.20), residues: 1744 helix: -0.81 (0.40), residues: 182 sheet: -1.23 (0.29), residues: 314 loop : -1.83 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 412 HIS 0.002 0.000 HIS D 5 PHE 0.022 0.001 PHE E 497 TYR 0.010 0.001 TYR E 60 ARG 0.003 0.000 ARG E 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7901 (tp) cc_final: 0.7095 (tp) REVERT: E 262 LEU cc_start: 0.9247 (mp) cc_final: 0.9032 (mm) REVERT: E 294 MET cc_start: 0.8323 (ppp) cc_final: 0.7862 (tpp) REVERT: E 333 CYS cc_start: 0.6784 (p) cc_final: 0.6514 (p) REVERT: E 405 ASN cc_start: 0.8818 (m-40) cc_final: 0.8447 (m110) REVERT: E 442 MET cc_start: 0.9256 (tpt) cc_final: 0.8888 (tpt) REVERT: E 504 MET cc_start: 0.8140 (mtp) cc_final: 0.7868 (mtm) REVERT: A 14 TYR cc_start: 0.7709 (t80) cc_final: 0.7363 (t80) REVERT: A 17 GLU cc_start: 0.8317 (pp20) cc_final: 0.8045 (pp20) REVERT: B 6 LEU cc_start: 0.9091 (mt) cc_final: 0.8824 (mt) REVERT: D 6 LEU cc_start: 0.9074 (mt) cc_final: 0.8871 (mt) REVERT: F 56 MET cc_start: 0.6945 (ttt) cc_final: 0.6699 (ttt) REVERT: F 256 PHE cc_start: 0.9362 (p90) cc_final: 0.9129 (p90) REVERT: F 333 CYS cc_start: 0.6677 (p) cc_final: 0.6346 (p) REVERT: F 442 MET cc_start: 0.9317 (tpt) cc_final: 0.8959 (tpt) REVERT: F 504 MET cc_start: 0.8206 (mtp) cc_final: 0.7931 (mtm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2065 time to fit residues: 29.4119 Evaluate side-chains 63 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 0.0000 chunk 7 optimal weight: 0.3980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.090627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062422 restraints weight = 186847.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063008 restraints weight = 97201.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064136 restraints weight = 59085.892| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14576 Z= 0.150 Angle : 0.594 7.693 19770 Z= 0.301 Chirality : 0.045 0.177 2140 Planarity : 0.005 0.109 2566 Dihedral : 5.331 75.580 1938 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.25 % Allowed : 0.19 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.22 (0.20), residues: 1744 helix: -0.80 (0.40), residues: 184 sheet: -1.20 (0.29), residues: 334 loop : -1.76 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 251 HIS 0.003 0.000 HIS E 247 PHE 0.022 0.001 PHE E 497 TYR 0.019 0.001 TYR C 14 ARG 0.007 0.000 ARG F 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.47 seconds wall clock time: 48 minutes 40.78 seconds (2920.78 seconds total)