Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 16:19:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_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_34018/08_2023/7yq3_34018_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_34018_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq3_34018/08_2023/7yq3_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-1.21rc1-5044/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: 11.02, per 1000 atoms: 0.76 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: 5.67 Conformation dependent library (CDL) restraints added in 3.2 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: 5.89 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: 4.11 Time building geometry restraints manager: 6.15 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: 8393 30.65 - 61.30: 409 61.30 - 91.95: 41 91.95 - 122.60: 0 122.60 - 153.25: 1 Dihedral angle restraints: 8844 sinusoidal: 3849 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 8841 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: 3.540 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: 0.020 Extract box with map and model: 14.410 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.690 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- 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 : 16.548 153.254 5499 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 % 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 *********************** 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 : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 222 average time/residue: 0.3204 time to fit residues: 99.5613 Evaluate side-chains 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3480 ------------------------------------------------------------------------------- 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: 0.5980 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.0030 chunk 156 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN E 21 HIS E 122 ASN E 123 ASN E 175 ASN E 230 ASN E 263 HIS E 295 ASN E 405 ASN 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 397 ASN F 405 ASN 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14830 Z= 0.188 Angle : 0.775 23.042 20230 Z= 0.356 Chirality : 0.045 0.168 2178 Planarity : 0.005 0.104 2521 Dihedral : 13.882 155.363 2131 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 1.80 % 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: -3.56 (0.18), residues: 1690 helix: -2.31 (0.33), residues: 181 sheet: -1.58 (0.26), residues: 363 loop : -2.83 (0.16), residues: 1146 *********************** 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 185 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 176 average time/residue: 0.2640 time to fit residues: 69.7355 Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1293 time to fit residues: 4.6154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 129 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN E 199 HIS E 627 HIS F 143 ASN F 209 HIS F 281 ASN F 406 GLN F 541 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14830 Z= 0.262 Angle : 0.784 21.807 20230 Z= 0.363 Chirality : 0.046 0.172 2178 Planarity : 0.005 0.108 2521 Dihedral : 13.617 151.308 2131 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer Outliers : 2.06 % 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: -3.32 (0.18), residues: 1690 helix: -1.88 (0.36), residues: 179 sheet: -1.48 (0.26), residues: 361 loop : -2.68 (0.16), residues: 1150 *********************** 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 169 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.2661 time to fit residues: 64.2266 Evaluate side-chains 153 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1939 time to fit residues: 8.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN E 546 GLN E 829 HIS ** 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: 0.6530 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14830 Z= 0.195 Angle : 0.750 20.195 20230 Z= 0.343 Chirality : 0.045 0.189 2178 Planarity : 0.004 0.105 2521 Dihedral : 13.489 150.703 2131 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.35 % 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: -3.08 (0.19), residues: 1690 helix: -1.47 (0.39), residues: 173 sheet: -1.32 (0.26), residues: 368 loop : -2.55 (0.16), residues: 1149 *********************** 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 157 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 152 average time/residue: 0.2693 time to fit residues: 61.4821 Evaluate side-chains 137 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1291 time to fit residues: 4.0202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN E 123 ASN E 230 ASN E 527 ASN F 440 HIS F 775 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14830 Z= 0.271 Angle : 0.770 19.742 20230 Z= 0.356 Chirality : 0.046 0.174 2178 Planarity : 0.004 0.107 2521 Dihedral : 13.534 152.433 2131 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 1.22 % 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: -3.00 (0.19), residues: 1690 helix: -1.48 (0.39), residues: 174 sheet: -1.27 (0.27), residues: 368 loop : -2.49 (0.17), residues: 1148 *********************** 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 151 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.767 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.2635 time to fit residues: 59.2564 Evaluate side-chains 136 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1475 time to fit residues: 5.5692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 160 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN E 230 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: 0.6522 moved from start: 0.2286 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= 0.168 Angle : 0.729 18.280 20230 Z= 0.331 Chirality : 0.044 0.162 2178 Planarity : 0.004 0.106 2521 Dihedral : 13.423 151.533 2131 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.16 % 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: -2.78 (0.19), residues: 1690 helix: -1.18 (0.40), residues: 166 sheet: -1.14 (0.27), residues: 366 loop : -2.34 (0.17), residues: 1158 *********************** 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 153 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.630 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 148 average time/residue: 0.2532 time to fit residues: 57.6603 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1245 time to fit residues: 3.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 GLN ** 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: 0.6515 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14830 Z= 0.172 Angle : 0.721 17.383 20230 Z= 0.328 Chirality : 0.044 0.158 2178 Planarity : 0.004 0.105 2521 Dihedral : 13.323 150.312 2131 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.90 % 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: -2.66 (0.19), residues: 1690 helix: -1.10 (0.41), residues: 166 sheet: -0.97 (0.27), residues: 359 loop : -2.28 (0.17), residues: 1165 *********************** 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 147 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.594 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 144 average time/residue: 0.2483 time to fit residues: 55.5422 Evaluate side-chains 137 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1541 time to fit residues: 4.0895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 5 HIS E 230 ASN F 148 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: 0.6580 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 14830 Z= 0.376 Angle : 0.815 18.185 20230 Z= 0.381 Chirality : 0.048 0.165 2178 Planarity : 0.005 0.108 2521 Dihedral : 13.521 154.035 2131 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer Outliers : 1.16 % 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: -1.45 (0.38), residues: 170 sheet: -1.19 (0.27), residues: 371 loop : -2.33 (0.17), residues: 1149 *********************** 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 140 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.703 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 0.2631 time to fit residues: 54.9294 Evaluate side-chains 131 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1384 time to fit residues: 4.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 21 ASN E 123 ASN E 230 ASN F 34 GLN F 784 GLN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2564 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= 0.259 Angle : 0.766 17.955 20230 Z= 0.353 Chirality : 0.046 0.176 2178 Planarity : 0.005 0.108 2521 Dihedral : 13.491 153.594 2131 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.45 % 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: -2.76 (0.19), residues: 1690 helix: -1.51 (0.38), residues: 175 sheet: -1.15 (0.27), residues: 369 loop : -2.26 (0.17), residues: 1146 *********************** 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 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 132 average time/residue: 0.2728 time to fit residues: 55.0206 Evaluate side-chains 126 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 14 optimal weight: 0.0470 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 145 optimal weight: 0.0570 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** 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: 0.6516 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 14830 Z= 0.156 Angle : 0.728 16.673 20230 Z= 0.330 Chirality : 0.044 0.180 2178 Planarity : 0.005 0.107 2521 Dihedral : 13.324 150.159 2131 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 0.64 % 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: -2.58 (0.20), residues: 1690 helix: -1.33 (0.39), residues: 177 sheet: -0.88 (0.27), residues: 354 loop : -2.19 (0.17), residues: 1159 ********************** 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 142 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 137 average time/residue: 0.2557 time to fit residues: 53.2217 Evaluate side-chains 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1337 time to fit residues: 2.8949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.0030 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 GLN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130841 restraints weight = 49232.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137130 restraints weight = 22972.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138973 restraints weight = 13527.911| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14830 Z= 0.173 Angle : 0.727 16.088 20230 Z= 0.329 Chirality : 0.044 0.197 2178 Planarity : 0.004 0.105 2521 Dihedral : 13.210 146.883 2131 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 0.32 % 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: -1.25 (0.39), residues: 176 sheet: -0.79 (0.27), residues: 359 loop : -2.13 (0.18), residues: 1155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.73 seconds wall clock time: 52 minutes 52.63 seconds (3172.63 seconds total)