Starting phenix.real_space_refine on Fri Feb 16 04:50:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/02_2024/7yq3_34018_updated.pdb" } resolution = 3.6 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= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 108 5.16 5 C 9047 2.51 5 N 2490 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 21": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E ARG 702": "NH1" <-> "NH2" Residue "E GLU 766": "OE1" <-> "OE2" Residue "E GLU 792": "OE1" <-> "OE2" Residue "E GLU 824": "OE1" <-> "OE2" Residue "E ARG 863": "NH1" <-> "NH2" Residue "E GLU 869": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F GLU 640": "OE1" <-> "OE2" Residue "F GLU 697": "OE1" <-> "OE2" Residue "F ARG 717": "NH1" <-> "NH2" Residue "F GLU 782": "OE1" <-> "OE2" Residue "F GLU 792": "OE1" <-> "OE2" Residue "F GLU 808": "OE1" <-> "OE2" Residue "F GLU 821": "OE1" <-> "OE2" Residue "F GLU 846": "OE1" <-> "OE2" Residue "F GLU 855": "OE1" <-> "OE2" Residue "F ARG 863": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14412 Number of models: 1 Model: "" Number of chains: 5 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: "E" Number of atoms: 6693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 830, 6686 Classifications: {'peptide': 830} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 784} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 830, 6686 Classifications: {'peptide': 830} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 784} Chain breaks: 3 bond proxies already assigned to first conformer: 6841 Chain: "F" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6694 Classifications: {'peptide': 831} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 785} Chain breaks: 3 Chain: "G" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 650 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 Time building chain proxies: 11.83, per 1000 atoms: 0.82 Number of scatterers: 14412 At special positions: 0 Unit cell: (95.23, 121.98, 189.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 28 15.00 O 2739 8.00 N 2490 7.00 C 9047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.04 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=1.89 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 683 " - pdb=" SG CYS F 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=1.75 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.04 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=1.82 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 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=2.02 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=2.06 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: 5.47 Conformation dependent library (CDL) restraints added in 4.0 seconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 22 sheets defined 10.1% alpha, 15.4% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 13 through 16 No H-bonds generated for 'chain 'A' and resid 13 through 16' Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'E' and resid 18 through 22 removed outlier: 4.003A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 256 through 266 Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 324 through 327 No H-bonds generated for 'chain 'E' and resid 324 through 327' Processing helix chain 'E' and resid 436 through 445 removed outlier: 3.651A pdb=" N HIS E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 641 No H-bonds generated for 'chain 'E' and resid 639 through 641' Processing helix chain 'E' and resid 690 through 709 removed outlier: 4.329A pdb=" N LEU E 693 " --> pdb=" O SER E 690 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 694 " --> pdb=" O GLN E 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 695 " --> pdb=" O ILE E 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER E 699 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP E 707 " --> pdb=" O THR E 704 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 708 " --> pdb=" O PHE E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 869 Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.660A pdb=" N LEU F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 256 through 269 removed outlier: 3.507A pdb=" N HIS F 263 " --> pdb=" O CYS F 259 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.615A pdb=" N GLU F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 442 Processing helix chain 'F' and resid 639 through 643 removed outlier: 3.776A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 713 removed outlier: 4.235A pdb=" N SER F 700 " --> pdb=" O LEU F 696 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS F 703 " --> pdb=" O SER F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 810 through 812 No H-bonds generated for 'chain 'F' and resid 810 through 812' Processing helix chain 'F' and resid 863 through 869 Processing sheet with id= A, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.912A pdb=" N GLN E 34 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE E 64 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU E 63 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 94 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 94 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG E 118 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE E 96 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU E 120 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS E 144 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 246 through 248 Processing sheet with id= C, first strand: chain 'E' and resid 278 through 280 Processing sheet with id= D, first strand: chain 'E' and resid 292 through 294 Processing sheet with id= E, first strand: chain 'E' and resid 318 through 321 removed outlier: 6.599A pdb=" N SER E 339 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 321 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 341 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 401 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LYS E 425 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR E 401 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 427 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU E 403 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS E 429 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 485 through 488 Processing sheet with id= G, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.626A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 602 through 605 Processing sheet with id= I, first strand: chain 'E' and resid 758 through 760 removed outlier: 3.768A pdb=" N TRP E 632 " --> pdb=" O PRO E 758 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY E 778 " --> pdb=" O GLN E 635 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 819 through 821 Processing sheet with id= K, first strand: chain 'E' and resid 857 through 861 removed outlier: 3.751A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR E 889 " --> pdb=" O VAL E 843 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR E 845 " --> pdb=" O ARG E 887 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG E 887 " --> pdb=" O TYR E 845 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL E 847 " --> pdb=" O ARG E 885 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG E 885 " --> pdb=" O VAL E 847 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR E 849 " --> pdb=" O SER E 883 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER E 883 " --> pdb=" O TYR E 849 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 33 through 36 removed outlier: 6.591A pdb=" N HIS F 144 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 231 through 233 Processing sheet with id= N, first strand: chain 'F' and resid 246 through 248 Processing sheet with id= O, first strand: chain 'F' and resid 292 through 294 Processing sheet with id= P, first strand: chain 'F' and resid 401 through 403 removed outlier: 6.373A pdb=" N PHE F 427 " --> pdb=" O ALA F 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 550 through 553 removed outlier: 3.531A pdb=" N LEU F 486 " --> pdb=" O ARG F 479 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 530 through 534 removed outlier: 6.864A pdb=" N LEU F 569 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE F 503 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS F 567 " --> pdb=" O PHE F 503 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 505 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE F 565 " --> pdb=" O LEU F 505 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR F 507 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA F 563 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU F 509 " --> pdb=" O GLN F 561 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN F 561 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 611 through 614 removed outlier: 3.811A pdb=" N LEU F 768 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 627 through 634 Processing sheet with id= U, first strand: chain 'F' and resid 819 through 822 Processing sheet with id= V, first strand: chain 'F' and resid 857 through 862 removed outlier: 4.332A pdb=" N LEU F 857 " --> pdb=" O TYR F 849 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR F 849 " --> pdb=" O LEU F 857 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 859 " --> pdb=" O VAL F 847 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR F 889 " --> pdb=" O VAL F 843 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR F 845 " --> pdb=" O ARG F 887 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG F 887 " --> pdb=" O TYR F 845 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL F 847 " --> pdb=" O ARG F 885 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG F 885 " --> pdb=" O VAL F 847 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR F 849 " --> pdb=" O SER F 883 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER F 883 " --> pdb=" O TYR F 849 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4373 1.34 - 1.46: 3806 1.46 - 1.59: 6466 1.59 - 1.71: 49 1.71 - 1.84: 136 Bond restraints: 14830 Sorted by residual: bond pdb=" C2' 85Y G 8 " pdb=" C1' 85Y G 8 " ideal model delta sigma weight residual 1.280 1.550 -0.270 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C2' 85Y G 15 " pdb=" C1' 85Y G 15 " ideal model delta sigma weight residual 1.280 1.550 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C2' 85Y G 6 " pdb=" C1' 85Y G 6 " ideal model delta sigma weight residual 1.280 1.544 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' 85Y G 23 " pdb=" C1' 85Y G 23 " ideal model delta sigma weight residual 1.280 1.540 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C2' 85Y G 17 " pdb=" C1' 85Y G 17 " ideal model delta sigma weight residual 1.280 1.539 -0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 91.21 - 100.45: 17 100.45 - 109.70: 2481 109.70 - 118.94: 9589 118.94 - 128.19: 7961 128.19 - 137.43: 182 Bond angle restraints: 20230 Sorted by residual: angle pdb=" N SER F 269 " pdb=" CA SER F 269 " pdb=" C SER F 269 " ideal model delta sigma weight residual 112.72 129.16 -16.44 1.14e+00 7.69e-01 2.08e+02 angle pdb=" N ASN E 230 " pdb=" CA ASN E 230 " pdb=" C ASN E 230 " ideal model delta sigma weight residual 111.07 126.15 -15.08 1.07e+00 8.73e-01 1.99e+02 angle pdb=" C PRO F 307 " pdb=" N CYS F 308 " pdb=" CA CYS F 308 " ideal model delta sigma weight residual 120.49 135.28 -14.79 1.42e+00 4.96e-01 1.08e+02 angle pdb=" C LYS F 265 " pdb=" CA LYS F 265 " pdb=" CB LYS F 265 " ideal model delta sigma weight residual 110.96 126.71 -15.75 1.54e+00 4.22e-01 1.05e+02 angle pdb=" C3' 85Y G 6 " pdb=" O3' 85Y G 6 " pdb=" P DA G 7 " ideal model delta sigma weight residual 120.20 134.86 -14.66 1.50e+00 4.44e-01 9.55e+01 ... (remaining 20225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 8429 30.65 - 61.30: 433 61.30 - 91.95: 41 91.95 - 122.60: 0 122.60 - 153.25: 1 Dihedral angle restraints: 8904 sinusoidal: 3909 harmonic: 4995 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 180.00 134.80 45.20 0 5.00e+00 4.00e-02 8.17e+01 dihedral pdb=" CB CYS E 524 " pdb=" SG CYS E 524 " pdb=" SG CYS F 524 " pdb=" CB CYS F 524 " ideal model delta sinusoidal sigma weight residual -86.00 -163.51 77.51 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS F 196 " pdb=" SG CYS F 196 " pdb=" SG CYS F 207 " pdb=" CB CYS F 207 " ideal model delta sinusoidal sigma weight residual -86.00 -162.69 76.69 1 1.00e+01 1.00e-02 7.39e+01 ... (remaining 8901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2127 0.149 - 0.298: 43 0.298 - 0.446: 5 0.446 - 0.595: 2 0.595 - 0.744: 1 Chirality restraints: 2178 Sorted by residual: chirality pdb=" CA SER F 269 " pdb=" N SER F 269 " pdb=" C SER F 269 " pdb=" CB SER F 269 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C4' DC G 28 " pdb=" C5' DC G 28 " pdb=" O4' DC G 28 " pdb=" C3' DC G 28 " both_signs ideal model delta sigma weight residual False -2.53 -1.97 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" CA LYS F 265 " pdb=" N LYS F 265 " pdb=" C LYS F 265 " pdb=" CB LYS F 265 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 2175 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 8 " -0.079 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO F 9 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO F 9 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 9 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO E 244 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 285 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO E 286 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 286 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 286 " -0.040 5.00e-02 4.00e+02 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 380 2.69 - 3.24: 12238 3.24 - 3.79: 21144 3.79 - 4.35: 26432 4.35 - 4.90: 44791 Nonbonded interactions: 104985 Sorted by model distance: nonbonded pdb=" OG1 THR F 325 " pdb=" OP2 DG G 11 " model vdw 2.136 2.440 nonbonded pdb=" O SER E 700 " pdb=" OG1 THR E 704 " model vdw 2.289 2.440 nonbonded pdb=" O SER F 210 " pdb=" OG SER F 210 " model vdw 2.293 2.440 nonbonded pdb=" O SER F 365 " pdb=" OG SER F 365 " model vdw 2.307 2.440 nonbonded pdb=" OG1 THR E 41 " pdb=" O TYR E 67 " model vdw 2.314 2.440 ... (remaining 104980 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 'E' and (resid 4 through 143 or resid 145 through 653 or resid 683 throug \ h 907)) selection = (chain 'F' and (resid 4 through 143 or resid 145 through 160 or resid 169 throug \ h 713 or resid 756 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: 4.320 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: 0.030 Extract box with map and model: 13.960 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 49.500 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 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 : 0.013 0.270 14830 Z= 0.718 Angle : 1.198 17.131 20230 Z= 0.613 Chirality : 0.065 0.744 2178 Planarity : 0.007 0.122 2521 Dihedral : 16.802 153.254 5559 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.32 % Allowed : 8.43 % Favored : 91.25 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -4.22 (0.16), residues: 1690 helix: -3.64 (0.22), residues: 187 sheet: -1.95 (0.25), residues: 364 loop : -3.15 (0.15), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 832 HIS 0.006 0.001 HIS F 829 PHE 0.023 0.002 PHE E 565 TYR 0.023 0.002 TYR E 507 ARG 0.004 0.000 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8560 (mpp80) cc_final: 0.8163 (mtm-85) REVERT: E 42 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7547 (ttp-110) REVERT: E 74 ASP cc_start: 0.6900 (t0) cc_final: 0.6686 (t0) REVERT: E 132 ASP cc_start: 0.7143 (t0) cc_final: 0.6829 (t0) REVERT: E 299 LEU cc_start: 0.8245 (tp) cc_final: 0.7629 (tt) REVERT: E 404 ASP cc_start: 0.7041 (t0) cc_final: 0.6837 (t0) REVERT: E 465 LYS cc_start: 0.8421 (mttm) cc_final: 0.8178 (mtmm) REVERT: E 482 PHE cc_start: 0.8312 (p90) cc_final: 0.8050 (p90) REVERT: E 600 ASP cc_start: 0.7399 (t0) cc_final: 0.7109 (t0) REVERT: E 646 TYR cc_start: 0.8536 (m-80) cc_final: 0.8016 (m-80) REVERT: E 652 LYS cc_start: 0.7588 (tppt) cc_final: 0.6927 (tptp) REVERT: E 695 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7774 (pm20) REVERT: E 709 LEU cc_start: 0.7073 (mm) cc_final: 0.6811 (mm) REVERT: E 776 PHE cc_start: 0.8005 (t80) cc_final: 0.7654 (t80) REVERT: E 806 MET cc_start: 0.7240 (mtt) cc_final: 0.7005 (mmp) REVERT: E 831 MET cc_start: 0.6590 (mmt) cc_final: 0.6250 (mmm) REVERT: E 873 ARG cc_start: 0.6318 (mtt180) cc_final: 0.6063 (mtm180) REVERT: F 45 ASP cc_start: 0.8837 (t0) cc_final: 0.8253 (t0) REVERT: F 47 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8264 (mmt90) REVERT: F 90 ASN cc_start: 0.8076 (t0) cc_final: 0.7775 (t0) REVERT: F 123 ASN cc_start: 0.8183 (t0) cc_final: 0.7899 (t0) REVERT: F 131 ILE cc_start: 0.8068 (mt) cc_final: 0.7861 (mt) REVERT: F 285 ILE cc_start: 0.7125 (mm) cc_final: 0.6785 (tt) REVERT: F 345 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7319 (mtm180) REVERT: F 479 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.7511 (ttp80) outliers start: 3 outliers final: 0 residues processed: 222 average time/residue: 0.3246 time to fit residues: 100.6606 Evaluate side-chains 146 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 HIS E 122 ASN E 123 ASN E 175 ASN E 230 ASN E 263 HIS E 295 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 452 GLN E 547 ASN ** E 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 ASN F 148 ASN F 168 ASN F 185 HIS F 209 HIS F 281 ASN F 397 ASN F 405 ASN F 406 GLN F 429 HIS F 610 GLN F 784 GLN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14830 Z= 0.238 Angle : 0.783 22.417 20230 Z= 0.363 Chirality : 0.046 0.172 2178 Planarity : 0.005 0.105 2521 Dihedral : 14.592 155.486 2191 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 1.74 % Allowed : 12.36 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -3.61 (0.18), residues: 1690 helix: -2.42 (0.32), residues: 189 sheet: -1.63 (0.25), residues: 365 loop : -2.84 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 832 HIS 0.006 0.001 HIS F 185 PHE 0.021 0.002 PHE B 25 TYR 0.021 0.001 TYR E 507 ARG 0.007 0.000 ARG E 554 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8635 (mpp80) cc_final: 0.8161 (mtm-85) REVERT: E 21 HIS cc_start: 0.7258 (m90) cc_final: 0.7012 (m90) REVERT: E 42 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7570 (ttp-110) REVERT: E 74 ASP cc_start: 0.6900 (t0) cc_final: 0.6652 (t0) REVERT: E 295 ASN cc_start: 0.5911 (t0) cc_final: 0.5647 (t0) REVERT: E 299 LEU cc_start: 0.8271 (tp) cc_final: 0.7803 (tt) REVERT: E 404 ASP cc_start: 0.7033 (t0) cc_final: 0.6830 (t0) REVERT: E 465 LYS cc_start: 0.8486 (mttm) cc_final: 0.8269 (mtmm) REVERT: E 482 PHE cc_start: 0.8358 (p90) cc_final: 0.7943 (p90) REVERT: E 600 ASP cc_start: 0.7450 (t0) cc_final: 0.7020 (t0) REVERT: E 709 LEU cc_start: 0.7111 (mm) cc_final: 0.6894 (mm) REVERT: E 776 PHE cc_start: 0.7995 (t80) cc_final: 0.7622 (t80) REVERT: E 806 MET cc_start: 0.7330 (mtt) cc_final: 0.6979 (mmp) REVERT: E 831 MET cc_start: 0.6703 (mmt) cc_final: 0.6412 (mmt) REVERT: E 873 ARG cc_start: 0.6269 (mtt180) cc_final: 0.6065 (mtm180) REVERT: F 11 MET cc_start: 0.8136 (ptp) cc_final: 0.7535 (ptp) REVERT: F 45 ASP cc_start: 0.8797 (t0) cc_final: 0.8269 (t0) REVERT: F 47 ARG cc_start: 0.8493 (mtt-85) cc_final: 0.7853 (ptt-90) REVERT: F 90 ASN cc_start: 0.7970 (t0) cc_final: 0.7646 (t0) REVERT: F 103 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: F 123 ASN cc_start: 0.8223 (t0) cc_final: 0.7952 (t0) REVERT: F 285 ILE cc_start: 0.6833 (mm) cc_final: 0.6429 (tt) REVERT: F 345 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7339 (mtm180) REVERT: F 479 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.7158 (ttp80) outliers start: 25 outliers final: 13 residues processed: 176 average time/residue: 0.2919 time to fit residues: 74.4104 Evaluate side-chains 157 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 795 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 HIS ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN F 123 ASN F 775 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14830 Z= 0.212 Angle : 0.756 21.664 20230 Z= 0.348 Chirality : 0.045 0.171 2178 Planarity : 0.004 0.108 2521 Dihedral : 14.269 151.299 2191 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.51 % Allowed : 14.80 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -3.27 (0.18), residues: 1690 helix: -1.78 (0.37), residues: 177 sheet: -1.50 (0.26), residues: 368 loop : -2.63 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 632 HIS 0.004 0.001 HIS F 275 PHE 0.021 0.002 PHE F 759 TYR 0.015 0.001 TYR E 507 ARG 0.005 0.000 ARG E 554 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8687 (mpp80) cc_final: 0.8168 (mtm-85) REVERT: E 11 MET cc_start: 0.7746 (mtp) cc_final: 0.7522 (mtp) REVERT: E 42 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7560 (ttp-110) REVERT: E 74 ASP cc_start: 0.6860 (t0) cc_final: 0.6612 (t0) REVERT: E 132 ASP cc_start: 0.7261 (t0) cc_final: 0.6960 (t0) REVERT: E 295 ASN cc_start: 0.5966 (t0) cc_final: 0.5170 (t0) REVERT: E 299 LEU cc_start: 0.8355 (tp) cc_final: 0.7706 (tp) REVERT: E 404 ASP cc_start: 0.7026 (t0) cc_final: 0.6809 (t0) REVERT: E 465 LYS cc_start: 0.8504 (mttm) cc_final: 0.8262 (mtmm) REVERT: E 482 PHE cc_start: 0.8366 (p90) cc_final: 0.7979 (p90) REVERT: E 600 ASP cc_start: 0.7551 (t0) cc_final: 0.7092 (t0) REVERT: E 652 LYS cc_start: 0.7361 (tppt) cc_final: 0.6982 (tptp) REVERT: E 776 PHE cc_start: 0.8007 (t80) cc_final: 0.7639 (t80) REVERT: E 806 MET cc_start: 0.7317 (mtt) cc_final: 0.6987 (mmp) REVERT: E 831 MET cc_start: 0.6723 (mmt) cc_final: 0.6495 (mmt) REVERT: E 873 ARG cc_start: 0.6412 (mtt180) cc_final: 0.6195 (mtm180) REVERT: F 11 MET cc_start: 0.8395 (ptp) cc_final: 0.7985 (ptp) REVERT: F 45 ASP cc_start: 0.8781 (t0) cc_final: 0.8271 (t0) REVERT: F 47 ARG cc_start: 0.8452 (mtt-85) cc_final: 0.7845 (ptt-90) REVERT: F 72 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6242 (tt) REVERT: F 90 ASN cc_start: 0.8019 (t0) cc_final: 0.7675 (t0) REVERT: F 98 MET cc_start: 0.7898 (ttm) cc_final: 0.7690 (ttm) REVERT: F 103 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: F 123 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (t0) REVERT: F 285 ILE cc_start: 0.6547 (mm) cc_final: 0.6177 (tt) REVERT: F 345 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7360 (mtm180) REVERT: F 412 TRP cc_start: 0.7409 (OUTLIER) cc_final: 0.6174 (m-90) REVERT: F 479 ARG cc_start: 0.7568 (tpp-160) cc_final: 0.6989 (ttp80) REVERT: F 501 LEU cc_start: 0.8482 (tt) cc_final: 0.8282 (mt) REVERT: F 832 TRP cc_start: 0.7076 (p90) cc_final: 0.6172 (p90) outliers start: 37 outliers final: 23 residues processed: 179 average time/residue: 0.2616 time to fit residues: 69.5066 Evaluate side-chains 169 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 757 ARG Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 613 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 630 VAL Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 627 HIS ** E 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 865 HIS F 123 ASN F 440 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14830 Z= 0.290 Angle : 0.779 20.932 20230 Z= 0.361 Chirality : 0.046 0.169 2178 Planarity : 0.005 0.106 2521 Dihedral : 14.254 152.450 2191 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.15 % Allowed : 16.34 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -3.16 (0.19), residues: 1690 helix: -1.67 (0.38), residues: 178 sheet: -1.48 (0.26), residues: 378 loop : -2.54 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 832 HIS 0.004 0.001 HIS F 275 PHE 0.022 0.002 PHE F 759 TYR 0.019 0.001 TYR E 708 ARG 0.006 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8645 (mpp80) cc_final: 0.8099 (mtm-85) REVERT: E 42 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7571 (ttp-110) REVERT: E 74 ASP cc_start: 0.6850 (t0) cc_final: 0.6599 (t0) REVERT: E 132 ASP cc_start: 0.7273 (t0) cc_final: 0.6974 (t0) REVERT: E 454 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.6944 (mmm160) REVERT: E 465 LYS cc_start: 0.8558 (mttm) cc_final: 0.8315 (mtmm) REVERT: E 482 PHE cc_start: 0.8360 (p90) cc_final: 0.7926 (p90) REVERT: E 600 ASP cc_start: 0.7554 (t0) cc_final: 0.7241 (t0) REVERT: E 776 PHE cc_start: 0.8016 (t80) cc_final: 0.7584 (t80) REVERT: E 806 MET cc_start: 0.7459 (mtt) cc_final: 0.7129 (mmp) REVERT: E 831 MET cc_start: 0.6750 (mmt) cc_final: 0.6521 (mmt) REVERT: E 873 ARG cc_start: 0.6408 (mtt180) cc_final: 0.6197 (mtm180) REVERT: F 45 ASP cc_start: 0.8791 (t0) cc_final: 0.8270 (t0) REVERT: F 47 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.7885 (ptt-90) REVERT: F 72 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6585 (tt) REVERT: F 90 ASN cc_start: 0.8007 (t0) cc_final: 0.7628 (t0) REVERT: F 98 MET cc_start: 0.7981 (ttm) cc_final: 0.7770 (ttm) REVERT: F 103 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: F 123 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7405 (t0) REVERT: F 285 ILE cc_start: 0.6663 (mm) cc_final: 0.6305 (tt) REVERT: F 345 ARG cc_start: 0.7816 (mtt-85) cc_final: 0.7384 (mtm180) REVERT: F 412 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.6270 (m-90) REVERT: F 479 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7026 (ttp80) REVERT: F 832 TRP cc_start: 0.7062 (p90) cc_final: 0.6225 (p90) REVERT: F 850 ARG cc_start: 0.5611 (ttp80) cc_final: 0.5078 (tmm160) outliers start: 47 outliers final: 26 residues processed: 177 average time/residue: 0.2649 time to fit residues: 69.8159 Evaluate side-chains 168 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN E 527 ASN E 865 HIS F 123 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14830 Z= 0.270 Angle : 0.767 20.476 20230 Z= 0.353 Chirality : 0.046 0.191 2178 Planarity : 0.004 0.108 2521 Dihedral : 14.237 153.188 2191 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.96 % Favored : 89.98 % Rotamer: Outliers : 3.02 % Allowed : 17.57 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -3.04 (0.19), residues: 1690 helix: -1.55 (0.39), residues: 174 sheet: -1.40 (0.26), residues: 373 loop : -2.47 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 832 HIS 0.004 0.001 HIS F 275 PHE 0.022 0.002 PHE F 759 TYR 0.020 0.001 TYR F 401 ARG 0.005 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8646 (mpp80) cc_final: 0.8098 (mtm-85) REVERT: E 42 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7570 (ttp-110) REVERT: E 74 ASP cc_start: 0.6843 (t0) cc_final: 0.6591 (t0) REVERT: E 132 ASP cc_start: 0.7269 (t0) cc_final: 0.7010 (t0) REVERT: E 295 ASN cc_start: 0.5650 (t0) cc_final: 0.5369 (t0) REVERT: E 465 LYS cc_start: 0.8515 (mttm) cc_final: 0.8259 (mtmm) REVERT: E 482 PHE cc_start: 0.8331 (p90) cc_final: 0.7944 (p90) REVERT: E 600 ASP cc_start: 0.7581 (t0) cc_final: 0.7257 (t0) REVERT: E 776 PHE cc_start: 0.8014 (t80) cc_final: 0.7584 (t80) REVERT: E 806 MET cc_start: 0.7362 (mtt) cc_final: 0.6997 (mmp) REVERT: E 831 MET cc_start: 0.6836 (mmt) cc_final: 0.6592 (mmt) REVERT: E 873 ARG cc_start: 0.6408 (mtt180) cc_final: 0.6177 (mtm180) REVERT: F 11 MET cc_start: 0.8408 (ptp) cc_final: 0.8056 (ptp) REVERT: F 45 ASP cc_start: 0.8783 (t0) cc_final: 0.8245 (t0) REVERT: F 47 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.7883 (ptt-90) REVERT: F 72 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6606 (tt) REVERT: F 90 ASN cc_start: 0.7996 (t0) cc_final: 0.7622 (t0) REVERT: F 98 MET cc_start: 0.7984 (ttm) cc_final: 0.7740 (ttm) REVERT: F 103 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: F 123 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7667 (t0) REVERT: F 285 ILE cc_start: 0.6695 (mm) cc_final: 0.6363 (tt) REVERT: F 345 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7408 (mtm180) REVERT: F 412 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.6202 (m-90) REVERT: F 479 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.7030 (ttp80) REVERT: F 832 TRP cc_start: 0.7058 (p90) cc_final: 0.6136 (p90) REVERT: F 850 ARG cc_start: 0.5587 (ttp80) cc_final: 0.5059 (tmm160) outliers start: 45 outliers final: 31 residues processed: 172 average time/residue: 0.2688 time to fit residues: 68.1756 Evaluate side-chains 173 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 757 ARG Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 820 HIS Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 160 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14830 Z= 0.163 Angle : 0.723 18.879 20230 Z= 0.329 Chirality : 0.044 0.181 2178 Planarity : 0.004 0.105 2521 Dihedral : 14.098 152.127 2191 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.45 % Allowed : 18.60 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -2.83 (0.19), residues: 1690 helix: -1.26 (0.41), residues: 169 sheet: -1.16 (0.27), residues: 366 loop : -2.38 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 183 HIS 0.004 0.001 HIS E 865 PHE 0.024 0.001 PHE F 759 TYR 0.013 0.001 TYR F 401 ARG 0.004 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8662 (mpp80) cc_final: 0.8129 (mtm-85) REVERT: E 42 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7544 (ttp-110) REVERT: E 74 ASP cc_start: 0.6799 (t0) cc_final: 0.6567 (t0) REVERT: E 132 ASP cc_start: 0.7363 (t0) cc_final: 0.7077 (t0) REVERT: E 295 ASN cc_start: 0.6000 (t0) cc_final: 0.5721 (t0) REVERT: E 454 ARG cc_start: 0.7001 (tpp-160) cc_final: 0.6782 (mmm160) REVERT: E 465 LYS cc_start: 0.8538 (mttm) cc_final: 0.8305 (mtmm) REVERT: E 482 PHE cc_start: 0.8384 (p90) cc_final: 0.7983 (p90) REVERT: E 600 ASP cc_start: 0.7579 (t0) cc_final: 0.7256 (t0) REVERT: E 776 PHE cc_start: 0.8014 (t80) cc_final: 0.7644 (t80) REVERT: E 806 MET cc_start: 0.7164 (mtt) cc_final: 0.6877 (mmp) REVERT: E 831 MET cc_start: 0.6748 (mmt) cc_final: 0.6500 (mmt) REVERT: E 873 ARG cc_start: 0.6302 (mtt180) cc_final: 0.6041 (mtm180) REVERT: E 885 ARG cc_start: 0.4643 (ttp80) cc_final: 0.4383 (ttp80) REVERT: F 11 MET cc_start: 0.8434 (ptp) cc_final: 0.8006 (ptp) REVERT: F 45 ASP cc_start: 0.8768 (t0) cc_final: 0.8264 (t0) REVERT: F 47 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.7877 (ptt-90) REVERT: F 72 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6293 (tt) REVERT: F 90 ASN cc_start: 0.7941 (t0) cc_final: 0.7577 (t0) REVERT: F 103 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: F 108 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6598 (t0) REVERT: F 123 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7440 (t0) REVERT: F 134 SER cc_start: 0.9015 (t) cc_final: 0.8733 (m) REVERT: F 285 ILE cc_start: 0.6543 (mm) cc_final: 0.6208 (tt) REVERT: F 345 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7402 (mtm180) REVERT: F 412 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.6145 (m-90) REVERT: F 479 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.6947 (ttp80) REVERT: F 760 GLU cc_start: 0.6848 (tt0) cc_final: 0.6535 (tt0) REVERT: F 832 TRP cc_start: 0.7000 (p90) cc_final: 0.6174 (p90) REVERT: F 850 ARG cc_start: 0.5677 (ttp80) cc_final: 0.5170 (tmm160) outliers start: 36 outliers final: 23 residues processed: 176 average time/residue: 0.2764 time to fit residues: 71.6256 Evaluate side-chains 170 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 820 HIS Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 0.0070 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 865 HIS F 123 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14830 Z= 0.212 Angle : 0.734 18.312 20230 Z= 0.334 Chirality : 0.045 0.166 2178 Planarity : 0.004 0.105 2521 Dihedral : 14.067 152.270 2191 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.90 % Allowed : 19.05 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -2.74 (0.19), residues: 1690 helix: -1.23 (0.41), residues: 167 sheet: -1.06 (0.27), residues: 361 loop : -2.32 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 632 HIS 0.003 0.001 HIS E 865 PHE 0.021 0.001 PHE F 759 TYR 0.014 0.001 TYR E 507 ARG 0.003 0.000 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.8659 (mpp80) cc_final: 0.8131 (mtm-85) REVERT: E 42 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7534 (ttp-110) REVERT: E 74 ASP cc_start: 0.6813 (t0) cc_final: 0.6577 (t0) REVERT: E 132 ASP cc_start: 0.7408 (t0) cc_final: 0.7125 (t0) REVERT: E 294 MET cc_start: 0.7687 (tpt) cc_final: 0.7388 (tpt) REVERT: E 295 ASN cc_start: 0.6009 (t0) cc_final: 0.5679 (t0) REVERT: E 454 ARG cc_start: 0.7013 (tpp-160) cc_final: 0.6741 (mmm160) REVERT: E 465 LYS cc_start: 0.8507 (mttm) cc_final: 0.8266 (mtmm) REVERT: E 482 PHE cc_start: 0.8355 (p90) cc_final: 0.7962 (p90) REVERT: E 600 ASP cc_start: 0.7647 (t0) cc_final: 0.7301 (t0) REVERT: E 776 PHE cc_start: 0.8016 (t80) cc_final: 0.7642 (t80) REVERT: E 806 MET cc_start: 0.7081 (mtt) cc_final: 0.6828 (mmp) REVERT: E 831 MET cc_start: 0.6561 (mmt) cc_final: 0.6320 (mmt) REVERT: E 873 ARG cc_start: 0.6243 (mtt180) cc_final: 0.5979 (mtm180) REVERT: E 885 ARG cc_start: 0.4678 (ttp80) cc_final: 0.4435 (ttp80) REVERT: F 11 MET cc_start: 0.8455 (ptp) cc_final: 0.8009 (ptp) REVERT: F 45 ASP cc_start: 0.8765 (t0) cc_final: 0.8248 (t0) REVERT: F 47 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.7898 (ptt-90) REVERT: F 72 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6354 (tt) REVERT: F 90 ASN cc_start: 0.7964 (t0) cc_final: 0.7623 (t0) REVERT: F 98 MET cc_start: 0.7961 (ttm) cc_final: 0.7687 (ttm) REVERT: F 103 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: F 108 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6485 (t0) REVERT: F 123 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7365 (t0) REVERT: F 285 ILE cc_start: 0.6639 (mm) cc_final: 0.6410 (tt) REVERT: F 345 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7444 (mtm180) REVERT: F 412 TRP cc_start: 0.7560 (OUTLIER) cc_final: 0.6147 (m-90) REVERT: F 479 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.6923 (ttp80) REVERT: F 760 GLU cc_start: 0.6894 (tt0) cc_final: 0.6605 (tt0) REVERT: F 832 TRP cc_start: 0.6975 (p90) cc_final: 0.6153 (p90) REVERT: F 850 ARG cc_start: 0.5664 (ttp80) cc_final: 0.5168 (tmm160) outliers start: 43 outliers final: 31 residues processed: 176 average time/residue: 0.2597 time to fit residues: 67.6358 Evaluate side-chains 177 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain E residue 820 HIS Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 0.0050 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN E 635 GLN E 865 HIS F 123 ASN F 405 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14830 Z= 0.425 Angle : 0.840 19.680 20230 Z= 0.396 Chirality : 0.049 0.165 2178 Planarity : 0.005 0.108 2521 Dihedral : 14.329 156.594 2191 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 3.02 % Allowed : 19.63 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -2.96 (0.19), residues: 1690 helix: -1.78 (0.38), residues: 177 sheet: -1.28 (0.27), residues: 366 loop : -2.37 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 632 HIS 0.005 0.001 HIS F 275 PHE 0.024 0.002 PHE E 427 TYR 0.017 0.002 TYR F 779 ARG 0.006 0.001 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8100 (tt0) cc_final: 0.7876 (tp40) REVERT: B 22 ARG cc_start: 0.8700 (mpp80) cc_final: 0.8104 (mtm-85) REVERT: E 42 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7538 (ttp-110) REVERT: E 74 ASP cc_start: 0.6874 (t0) cc_final: 0.6616 (t0) REVERT: E 294 MET cc_start: 0.7624 (tpt) cc_final: 0.7381 (tpt) REVERT: E 295 ASN cc_start: 0.5923 (t0) cc_final: 0.5572 (t0) REVERT: E 441 LYS cc_start: 0.6930 (mmmm) cc_final: 0.6661 (tppt) REVERT: E 465 LYS cc_start: 0.8573 (mttm) cc_final: 0.8249 (mtmm) REVERT: E 482 PHE cc_start: 0.8315 (p90) cc_final: 0.7890 (p90) REVERT: E 600 ASP cc_start: 0.7745 (t0) cc_final: 0.7368 (t0) REVERT: E 776 PHE cc_start: 0.8086 (t80) cc_final: 0.7572 (t80) REVERT: E 806 MET cc_start: 0.7291 (mtt) cc_final: 0.6961 (mmp) REVERT: E 831 MET cc_start: 0.6665 (mmt) cc_final: 0.6297 (mmt) REVERT: E 873 ARG cc_start: 0.6426 (mtt180) cc_final: 0.6184 (mtm180) REVERT: F 45 ASP cc_start: 0.8817 (t0) cc_final: 0.8274 (t0) REVERT: F 47 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.7907 (ptt-90) REVERT: F 98 MET cc_start: 0.8069 (ttm) cc_final: 0.7800 (ttm) REVERT: F 103 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: F 108 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6637 (t0) REVERT: F 123 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7443 (t0) REVERT: F 131 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8097 (pt) REVERT: F 285 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6814 (tt) REVERT: F 345 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7481 (mtm180) REVERT: F 412 TRP cc_start: 0.7723 (OUTLIER) cc_final: 0.6291 (m-90) REVERT: F 479 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7026 (ttp80) outliers start: 45 outliers final: 32 residues processed: 177 average time/residue: 0.2665 time to fit residues: 70.1262 Evaluate side-chains 177 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 812 ASP Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 455 ASN Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 101 optimal weight: 0.0040 chunk 163 optimal weight: 0.9980 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN E 865 HIS F 123 ASN F 405 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14830 Z= 0.164 Angle : 0.725 17.951 20230 Z= 0.329 Chirality : 0.044 0.158 2178 Planarity : 0.004 0.108 2521 Dihedral : 14.088 152.897 2191 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.45 % Allowed : 20.21 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -2.67 (0.19), residues: 1690 helix: -1.40 (0.40), residues: 171 sheet: -0.98 (0.27), residues: 361 loop : -2.24 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 632 HIS 0.004 0.001 HIS E 865 PHE 0.025 0.001 PHE F 759 TYR 0.014 0.001 TYR F 401 ARG 0.004 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8088 (tt0) cc_final: 0.7879 (tp40) REVERT: B 22 ARG cc_start: 0.8691 (mpp80) cc_final: 0.8156 (mtm-85) REVERT: E 42 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7547 (ttp-110) REVERT: E 74 ASP cc_start: 0.6802 (t0) cc_final: 0.6590 (t0) REVERT: E 295 ASN cc_start: 0.5799 (t0) cc_final: 0.5487 (t0) REVERT: E 454 ARG cc_start: 0.6999 (tpp-160) cc_final: 0.6789 (mmm160) REVERT: E 465 LYS cc_start: 0.8485 (mttm) cc_final: 0.8235 (mtmm) REVERT: E 482 PHE cc_start: 0.8358 (p90) cc_final: 0.7972 (p90) REVERT: E 600 ASP cc_start: 0.7681 (t0) cc_final: 0.7335 (t0) REVERT: E 776 PHE cc_start: 0.8112 (t80) cc_final: 0.7592 (t80) REVERT: E 831 MET cc_start: 0.6602 (mmt) cc_final: 0.6279 (mmt) REVERT: E 873 ARG cc_start: 0.6284 (mtt180) cc_final: 0.6037 (mtm180) REVERT: E 885 ARG cc_start: 0.4683 (ttp80) cc_final: 0.4423 (ttp80) REVERT: F 45 ASP cc_start: 0.8858 (t0) cc_final: 0.8386 (t0) REVERT: F 72 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6453 (tt) REVERT: F 98 MET cc_start: 0.7976 (ttm) cc_final: 0.7675 (ttm) REVERT: F 103 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: F 108 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6446 (t0) REVERT: F 123 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7259 (t0) REVERT: F 285 ILE cc_start: 0.6630 (mm) cc_final: 0.6422 (tt) REVERT: F 345 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7511 (mtm180) REVERT: F 412 TRP cc_start: 0.7592 (OUTLIER) cc_final: 0.6033 (m-90) REVERT: F 479 ARG cc_start: 0.7664 (tpp-160) cc_final: 0.6839 (ttp80) REVERT: F 760 GLU cc_start: 0.6779 (tt0) cc_final: 0.6498 (tt0) REVERT: F 832 TRP cc_start: 0.6975 (p90) cc_final: 0.6138 (p90) outliers start: 36 outliers final: 26 residues processed: 173 average time/residue: 0.2710 time to fit residues: 69.3586 Evaluate side-chains 168 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 CYS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 187 HIS Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 0.0570 chunk 14 optimal weight: 0.0870 chunk 105 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 145 optimal weight: 0.0970 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 865 HIS F 34 GLN F 123 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14830 Z= 0.142 Angle : 0.712 16.824 20230 Z= 0.321 Chirality : 0.043 0.158 2178 Planarity : 0.004 0.105 2521 Dihedral : 13.907 149.465 2191 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.12 % Allowed : 21.04 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: -2.50 (0.20), residues: 1690 helix: -1.12 (0.42), residues: 165 sheet: -0.81 (0.27), residues: 366 loop : -2.17 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 632 HIS 0.004 0.000 HIS E 865 PHE 0.022 0.001 PHE F 759 TYR 0.013 0.001 TYR E 507 ARG 0.004 0.000 ARG E 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8042 (tt0) cc_final: 0.7836 (tp40) REVERT: B 22 ARG cc_start: 0.8652 (mpp80) cc_final: 0.8157 (mtm-85) REVERT: E 42 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7509 (ttp-110) REVERT: E 295 ASN cc_start: 0.5768 (t0) cc_final: 0.5555 (t0) REVERT: E 313 HIS cc_start: 0.7588 (t-90) cc_final: 0.6982 (m170) REVERT: E 465 LYS cc_start: 0.8522 (mttm) cc_final: 0.8287 (mtmm) REVERT: E 482 PHE cc_start: 0.8349 (p90) cc_final: 0.7958 (p90) REVERT: E 600 ASP cc_start: 0.7722 (t0) cc_final: 0.7335 (t0) REVERT: E 776 PHE cc_start: 0.8062 (t80) cc_final: 0.7652 (t80) REVERT: E 831 MET cc_start: 0.6570 (mmt) cc_final: 0.6237 (mmt) REVERT: E 873 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5953 (mtm180) REVERT: E 885 ARG cc_start: 0.4610 (ttp80) cc_final: 0.4348 (ttp80) REVERT: F 45 ASP cc_start: 0.8804 (t0) cc_final: 0.8367 (t0) REVERT: F 72 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6354 (tt) REVERT: F 98 MET cc_start: 0.7956 (ttm) cc_final: 0.7663 (ttm) REVERT: F 108 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6526 (t0) REVERT: F 123 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7215 (t0) REVERT: F 134 SER cc_start: 0.8996 (t) cc_final: 0.8696 (m) REVERT: F 345 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7443 (mtm180) REVERT: F 412 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.6141 (m-90) REVERT: F 479 ARG cc_start: 0.7660 (tpp-160) cc_final: 0.6845 (ttp80) REVERT: F 760 GLU cc_start: 0.6738 (tt0) cc_final: 0.6314 (tt0) REVERT: F 832 TRP cc_start: 0.6951 (p90) cc_final: 0.6212 (p90) outliers start: 31 outliers final: 23 residues processed: 173 average time/residue: 0.2583 time to fit residues: 66.3491 Evaluate side-chains 167 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 535 ASP Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 620 ASP Chi-restraints excluded: chain E residue 763 VAL Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 844 LEU Chi-restraints excluded: chain F residue 859 LEU Chi-restraints excluded: chain F residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0060 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.0050 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 HIS E 865 HIS F 143 ASN F 148 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.194101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139842 restraints weight = 52665.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145257 restraints weight = 26160.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147487 restraints weight = 14288.298| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14830 Z= 0.165 Angle : 0.710 16.610 20230 Z= 0.319 Chirality : 0.044 0.155 2178 Planarity : 0.004 0.105 2521 Dihedral : 13.832 147.181 2191 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.25 % Allowed : 21.11 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.12 % Twisted Proline : 1.14 % 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: 1690 helix: -1.24 (0.40), residues: 171 sheet: -0.73 (0.28), residues: 366 loop : -2.16 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 632 HIS 0.004 0.001 HIS E 865 PHE 0.022 0.001 PHE F 759 TYR 0.014 0.001 TYR E 507 ARG 0.004 0.000 ARG F 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.18 seconds wall clock time: 57 minutes 14.26 seconds (3434.26 seconds total)