Starting phenix.real_space_refine on Fri Feb 16 04:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq5_34020/02_2024/7yq5_34020_updated.pdb" } resolution = 4.27 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 242 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 104 5.16 5 C 8839 2.51 5 N 2431 2.21 5 O 2663 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 13": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 391": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 409": "NH1" <-> "NH2" Residue "F GLU 444": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F GLU 640": "OE1" <-> "OE2" Residue "F GLU 698": "OE1" <-> "OE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 331": "NH1" <-> "NH2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E GLU 443": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 517": "OE1" <-> "OE2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E GLU 643": "OE1" <-> "OE2" 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" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14067 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: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 577 Classifications: {'DNA': 21, 'RNA': 3} Modifications used: {'rna2p': 1, 'rna3p': 2} Link IDs: {'rna2p': 1, 'rna3p': 22} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 6 Chain: "F" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6676 Classifications: {'peptide': 828} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 780} Chain breaks: 3 Chain: "E" Number of atoms: 6439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 799, 6432 Classifications: {'peptide': 799} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 754} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 799, 6432 Classifications: {'peptide': 799} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 754} Chain breaks: 2 bond proxies already assigned to first conformer: 6583 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: 10.75, per 1000 atoms: 0.76 Number of scatterers: 14067 At special positions: 0 Unit cell: (98.6, 139.4, 189.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 24 15.00 F 6 9.00 O 2663 8.00 N 2431 7.00 C 8839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.01 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.02 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.02 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.02 Simple disulfide: pdb=" SG CYS F 524 " - pdb=" SG CYS E 524 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.04 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 3.7 seconds 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 23 sheets defined 8.8% alpha, 14.9% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.603A pdb=" N VAL B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 15 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 17 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 18 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 removed outlier: 3.731A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' 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 257 through 265 removed outlier: 3.877A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS F 263 " --> pdb=" O CYS F 259 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS F 264 " --> pdb=" O GLN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 removed outlier: 4.927A pdb=" N GLU F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 357 Processing helix chain 'F' and resid 639 through 643 removed outlier: 3.777A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 713 removed outlier: 3.599A pdb=" N SER F 699 " --> pdb=" O GLU F 695 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN F 711 " --> pdb=" O ASP F 707 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 712 " --> pdb=" O TYR F 708 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 713 " --> pdb=" O LEU F 709 " (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 helix chain 'E' and resid 18 through 22 removed outlier: 3.509A pdb=" N HIS E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 22' Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.697A pdb=" N GLN E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS E 264 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) No H-bonds generated for '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 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 436 through 445 removed outlier: 3.610A pdb=" N MET E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' 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 863 through 869 Processing sheet with id= A, first strand: chain 'F' and resid 33 through 36 removed outlier: 6.197A pdb=" N HIS F 144 " --> pdb=" O ILE F 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 231 through 233 Processing sheet with id= C, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.590A pdb=" N ARG F 252 " --> pdb=" O PHE F 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 278 through 280 removed outlier: 3.591A pdb=" N HIS F 280 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 283 " --> pdb=" O HIS F 280 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 292 through 295 removed outlier: 3.661A pdb=" N LEU F 300 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 400 through 402 Processing sheet with id= G, first strand: chain 'F' and resid 550 through 553 removed outlier: 3.520A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG F 479 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG F 488 " --> pdb=" O TYR F 477 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 530 through 535 removed outlier: 3.859A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 534 " --> pdb=" O PHE F 503 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU F 569 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE F 503 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS F 567 " --> pdb=" O PHE F 503 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU F 505 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE F 565 " --> pdb=" O LEU F 505 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR F 507 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA F 563 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU F 509 " --> pdb=" O GLN F 561 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN F 561 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing sheet with id= I, 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= J, first strand: chain 'F' and resid 627 through 634 Processing sheet with id= K, first strand: chain 'F' and resid 819 through 822 Processing sheet with id= L, 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: 3.522A 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: 6.745A 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: 4.482A 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) Processing sheet with id= M, first strand: chain 'E' and resid 11 through 14 Processing sheet with id= N, first strand: chain 'E' and resid 246 through 248 removed outlier: 3.540A pdb=" N TYR E 246 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 278 through 280 Processing sheet with id= P, first strand: chain 'E' and resid 292 through 294 removed outlier: 3.866A pdb=" N THR E 293 " --> pdb=" O THR E 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 302 " --> pdb=" O THR E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 318 through 321 removed outlier: 7.229A pdb=" N SER E 339 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE E 321 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 341 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 486 through 488 removed outlier: 3.558A pdb=" N LEU E 487 " --> pdb=" O TRP E 551 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP E 551 " --> pdb=" O LEU E 487 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 532 through 534 removed outlier: 3.830A pdb=" N ILE E 534 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE E 503 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 602 through 605 Processing sheet with id= U, 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: 3.678A 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: 4.482A pdb=" N GLY E 778 " --> pdb=" O GLN E 635 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 819 through 821 Processing sheet with id= W, 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: 6.743A 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: 6.727A 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) 172 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 4.27 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: 1.18 - 1.31: 2290 1.31 - 1.44: 4104 1.44 - 1.58: 7884 1.58 - 1.71: 57 1.71 - 1.84: 134 Bond restraints: 14469 Sorted by residual: bond pdb=" O4' AF2 G 19 " pdb=" C1' AF2 G 19 " ideal model delta sigma weight residual 1.599 1.302 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" O4' AF2 G 12 " pdb=" C1' AF2 G 12 " ideal model delta sigma weight residual 1.599 1.304 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" O4' AF2 G 2 " pdb=" C1' AF2 G 2 " ideal model delta sigma weight residual 1.599 1.310 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C2' CFZ G 6 " pdb=" C1' CFZ G 6 " ideal model delta sigma weight residual 1.580 1.292 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C2' CFZ G 22 " pdb=" C1' CFZ G 22 " ideal model delta sigma weight residual 1.580 1.296 0.284 2.00e-02 2.50e+03 2.02e+02 ... (remaining 14464 not shown) Histogram of bond angle deviations from ideal: 96.91 - 105.62: 432 105.62 - 114.34: 8207 114.34 - 123.05: 9766 123.05 - 131.76: 1276 131.76 - 140.48: 46 Bond angle restraints: 19727 Sorted by residual: angle pdb=" C LYS F 310 " pdb=" N VAL F 311 " pdb=" CA VAL F 311 " ideal model delta sigma weight residual 121.70 132.87 -11.17 1.80e+00 3.09e-01 3.85e+01 angle pdb=" CA LEU E 299 " pdb=" CB LEU E 299 " pdb=" CG LEU E 299 " ideal model delta sigma weight residual 116.30 137.30 -21.00 3.50e+00 8.16e-02 3.60e+01 angle pdb=" C1' OMG G 13 " pdb=" N9 OMG G 13 " pdb=" C4 OMG G 13 " ideal model delta sigma weight residual 108.29 125.41 -17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" C VAL F 763 " pdb=" N ASN F 764 " pdb=" CA ASN F 764 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C LEU F 599 " pdb=" N ASP F 600 " pdb=" CA ASP F 600 " ideal model delta sigma weight residual 121.80 134.58 -12.78 2.44e+00 1.68e-01 2.74e+01 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 8345 34.89 - 69.78: 305 69.78 - 104.68: 39 104.68 - 139.57: 1 139.57 - 174.46: 6 Dihedral angle restraints: 8696 sinusoidal: 3803 harmonic: 4893 Sorted by residual: dihedral pdb=" CB CYS E 192 " pdb=" SG CYS E 192 " pdb=" SG CYS E 201 " pdb=" CB CYS E 201 " ideal model delta sinusoidal sigma weight residual 93.00 -178.86 -88.14 1 1.00e+01 1.00e-02 9.29e+01 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 180.00 132.22 47.78 0 5.00e+00 4.00e-02 9.13e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 155 " pdb=" CB CYS F 155 " ideal model delta sinusoidal sigma weight residual 93.00 179.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 8693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1743 0.083 - 0.167: 321 0.167 - 0.250: 31 0.250 - 0.334: 7 0.334 - 0.417: 5 Chirality restraints: 2107 Sorted by residual: chirality pdb=" C3' AF2 G 12 " pdb=" C4' AF2 G 12 " pdb=" O3' AF2 G 12 " pdb=" C2' AF2 G 12 " both_signs ideal model delta sigma weight residual False -2.47 -2.05 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C3' DUZ G 14 " pdb=" C4' DUZ G 14 " pdb=" O3' DUZ G 14 " pdb=" C2' DUZ G 14 " both_signs ideal model delta sigma weight residual False -2.39 -1.98 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 2104 not shown) Planarity restraints: 2474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG G 13 " 0.036 2.00e-02 2.50e+03 5.47e-01 6.74e+03 pdb=" C4' OMG G 13 " 0.426 2.00e-02 2.50e+03 pdb=" O4' OMG G 13 " 0.531 2.00e-02 2.50e+03 pdb=" C3' OMG G 13 " -0.577 2.00e-02 2.50e+03 pdb=" O3' OMG G 13 " -0.555 2.00e-02 2.50e+03 pdb=" C2' OMG G 13 " -0.199 2.00e-02 2.50e+03 pdb=" O2' OMG G 13 " 0.909 2.00e-02 2.50e+03 pdb=" C1' OMG G 13 " 0.244 2.00e-02 2.50e+03 pdb=" N9 OMG G 13 " -0.815 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG G 11 " -0.622 2.00e-02 2.50e+03 4.92e-01 5.44e+03 pdb=" C4' OMG G 11 " 0.239 2.00e-02 2.50e+03 pdb=" O4' OMG G 11 " 0.344 2.00e-02 2.50e+03 pdb=" C3' OMG G 11 " -0.220 2.00e-02 2.50e+03 pdb=" O3' OMG G 11 " 0.894 2.00e-02 2.50e+03 pdb=" C2' OMG G 11 " -0.606 2.00e-02 2.50e+03 pdb=" O2' OMG G 11 " -0.497 2.00e-02 2.50e+03 pdb=" C1' OMG G 11 " 0.380 2.00e-02 2.50e+03 pdb=" N9 OMG G 11 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC G 21 " 0.018 2.00e-02 2.50e+03 4.59e-01 4.74e+03 pdb=" C4' OMC G 21 " 0.385 2.00e-02 2.50e+03 pdb=" O4' OMC G 21 " 0.403 2.00e-02 2.50e+03 pdb=" C3' OMC G 21 " -0.568 2.00e-02 2.50e+03 pdb=" O3' OMC G 21 " -0.374 2.00e-02 2.50e+03 pdb=" C2' OMC G 21 " -0.271 2.00e-02 2.50e+03 pdb=" O2' OMC G 21 " 0.767 2.00e-02 2.50e+03 pdb=" C1' OMC G 21 " 0.265 2.00e-02 2.50e+03 pdb=" N1 OMC G 21 " -0.625 2.00e-02 2.50e+03 ... (remaining 2471 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2998 2.78 - 3.31: 11548 3.31 - 3.84: 21630 3.84 - 4.37: 23512 4.37 - 4.90: 40797 Nonbonded interactions: 100485 Sorted by model distance: nonbonded pdb=" O5' 85Y G 10 " pdb=" O4' 85Y G 10 " model vdw 2.256 2.432 nonbonded pdb=" OG SER F 573 " pdb=" OE1 GLU F 575 " model vdw 2.301 2.440 nonbonded pdb=" OG SER E 339 " pdb=" O TYR E 367 " model vdw 2.309 2.440 nonbonded pdb=" OD2 ASP F 812 " pdb=" OG SER F 890 " model vdw 2.314 2.440 nonbonded pdb=" N3 DUZ G 14 " pdb=" O21 85Y G 16 " model vdw 2.316 2.520 ... (remaining 100480 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 907)) selection = (chain 'F' and (resid 4 through 143 or resid 145 through 160 or resid 169 throug \ h 686 or resid 700 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: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 16.450 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 47.280 Find NCS groups from input model: 0.850 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 : 0.014 0.297 14469 Z= 0.754 Angle : 1.241 21.004 19727 Z= 0.616 Chirality : 0.067 0.417 2107 Planarity : 0.019 0.547 2474 Dihedral : 17.988 174.460 5422 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.59 % Allowed : 9.34 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % Twisted General : 0.19 % 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: -4.10 (0.17), residues: 1658 helix: -4.76 (0.17), residues: 131 sheet: -1.71 (0.26), residues: 357 loop : -3.03 (0.15), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 412 HIS 0.007 0.001 HIS E 548 PHE 0.021 0.003 PHE F 565 TYR 0.024 0.002 TYR F 60 ARG 0.012 0.001 ARG F 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 276 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 230 ASN cc_start: 0.7954 (t0) cc_final: 0.7547 (t0) REVERT: F 593 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6270 (p) REVERT: E 38 MET cc_start: 0.6226 (mtm) cc_final: 0.5947 (ptp) outliers start: 8 outliers final: 0 residues processed: 282 average time/residue: 0.3301 time to fit residues: 129.6794 Evaluate side-chains 136 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 chunk 79 optimal weight: 30.0000 chunk 97 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 overall best weight: 2.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS F 148 ASN F 209 HIS ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 610 GLN ** F 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 829 HIS E 34 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 14469 Z= 0.383 Angle : 1.014 15.092 19727 Z= 0.516 Chirality : 0.054 0.519 2107 Planarity : 0.007 0.125 2474 Dihedral : 17.029 175.398 2123 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % Twisted General : 0.13 % 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: -3.55 (0.18), residues: 1658 helix: -3.68 (0.30), residues: 128 sheet: -1.35 (0.26), residues: 362 loop : -2.73 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 412 HIS 0.008 0.001 HIS B 5 PHE 0.017 0.002 PHE E 506 TYR 0.023 0.002 TYR E 60 ARG 0.008 0.001 ARG F 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 457 ILE cc_start: 0.6296 (mm) cc_final: 0.6070 (mm) REVERT: F 527 ASN cc_start: 0.7892 (t0) cc_final: 0.7613 (t0) REVERT: E 98 MET cc_start: 0.8782 (mmt) cc_final: 0.8038 (mmt) REVERT: E 442 MET cc_start: 0.8833 (tpt) cc_final: 0.8564 (tpt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2767 time to fit residues: 66.1731 Evaluate side-chains 96 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 546 GLN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14469 Z= 0.252 Angle : 0.879 13.258 19727 Z= 0.456 Chirality : 0.049 0.380 2107 Planarity : 0.007 0.121 2474 Dihedral : 16.403 165.298 2123 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.20 % Allowed : 4.87 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -3.14 (0.19), residues: 1658 helix: -2.78 (0.42), residues: 116 sheet: -1.10 (0.26), residues: 382 loop : -2.54 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 412 HIS 0.008 0.001 HIS F 829 PHE 0.014 0.002 PHE F 497 TYR 0.012 0.001 TYR E 91 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 504 MET cc_start: 0.8282 (mmm) cc_final: 0.7913 (mmm) REVERT: F 527 ASN cc_start: 0.7898 (t0) cc_final: 0.7660 (t0) REVERT: E 98 MET cc_start: 0.8824 (mmt) cc_final: 0.8172 (mmt) REVERT: E 548 HIS cc_start: 0.5079 (m90) cc_final: 0.4233 (m90) REVERT: E 831 MET cc_start: 0.8068 (ppp) cc_final: 0.7336 (ppp) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.2367 time to fit residues: 54.2519 Evaluate side-chains 85 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 79 optimal weight: 40.0000 chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 829 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14469 Z= 0.313 Angle : 0.897 12.931 19727 Z= 0.465 Chirality : 0.050 0.363 2107 Planarity : 0.007 0.120 2474 Dihedral : 16.474 165.374 2123 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.97 (0.19), residues: 1658 helix: -2.57 (0.42), residues: 126 sheet: -0.80 (0.27), residues: 370 loop : -2.48 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 412 HIS 0.007 0.001 HIS F 264 PHE 0.017 0.002 PHE F 89 TYR 0.015 0.001 TYR E 91 ARG 0.006 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 504 MET cc_start: 0.8275 (mmm) cc_final: 0.7698 (mmm) REVERT: F 527 ASN cc_start: 0.8054 (t0) cc_final: 0.7823 (t0) REVERT: E 442 MET cc_start: 0.8919 (tpt) cc_final: 0.8442 (tpt) REVERT: E 548 HIS cc_start: 0.5369 (m90) cc_final: 0.4590 (m90) REVERT: E 831 MET cc_start: 0.8090 (ppp) cc_final: 0.7478 (ppp) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.2456 time to fit residues: 47.7803 Evaluate side-chains 84 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS F 829 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14469 Z= 0.192 Angle : 0.834 12.534 19727 Z= 0.434 Chirality : 0.048 0.366 2107 Planarity : 0.006 0.117 2474 Dihedral : 16.192 161.881 2123 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.13 % Allowed : 1.97 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.74 (0.19), residues: 1658 helix: -2.23 (0.44), residues: 121 sheet: -0.72 (0.27), residues: 375 loop : -2.32 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 412 HIS 0.006 0.001 HIS B 10 PHE 0.014 0.002 PHE F 497 TYR 0.011 0.001 TYR E 430 ARG 0.009 0.000 ARG E 875 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 97 GLU cc_start: 0.8045 (tp30) cc_final: 0.7611 (tm-30) REVERT: F 504 MET cc_start: 0.8216 (mmm) cc_final: 0.7678 (mmm) REVERT: E 98 MET cc_start: 0.8901 (mmt) cc_final: 0.8695 (mmt) REVERT: E 442 MET cc_start: 0.8863 (tpt) cc_final: 0.8414 (tpt) REVERT: E 504 MET cc_start: 0.8519 (mtm) cc_final: 0.8278 (mtt) REVERT: E 548 HIS cc_start: 0.5039 (m90) cc_final: 0.4479 (m90) REVERT: E 831 MET cc_start: 0.8050 (ppp) cc_final: 0.7611 (ppp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2335 time to fit residues: 47.3189 Evaluate side-chains 82 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 HIS ** 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: 0.7361 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14469 Z= 0.202 Angle : 0.824 12.653 19727 Z= 0.430 Chirality : 0.048 0.365 2107 Planarity : 0.006 0.117 2474 Dihedral : 16.051 162.280 2123 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.59 (0.20), residues: 1658 helix: -2.01 (0.45), residues: 120 sheet: -0.61 (0.27), residues: 380 loop : -2.23 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 412 HIS 0.007 0.001 HIS F 187 PHE 0.013 0.001 PHE F 497 TYR 0.010 0.001 TYR E 430 ARG 0.006 0.000 ARG E 875 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 97 GLU cc_start: 0.8081 (tp30) cc_final: 0.7607 (tm-30) REVERT: F 504 MET cc_start: 0.8242 (mmm) cc_final: 0.7805 (mmm) REVERT: E 98 MET cc_start: 0.8956 (mmt) cc_final: 0.8717 (mmt) REVERT: E 442 MET cc_start: 0.8869 (tpt) cc_final: 0.8459 (tpt) REVERT: E 504 MET cc_start: 0.8492 (mtm) cc_final: 0.8247 (mtt) REVERT: E 548 HIS cc_start: 0.4992 (m90) cc_final: 0.4548 (m90) REVERT: E 831 MET cc_start: 0.8120 (ppp) cc_final: 0.7818 (ppp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2430 time to fit residues: 46.6549 Evaluate side-chains 80 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14469 Z= 0.238 Angle : 0.835 12.960 19727 Z= 0.435 Chirality : 0.048 0.367 2107 Planarity : 0.006 0.117 2474 Dihedral : 16.027 162.515 2123 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.54 (0.20), residues: 1658 helix: -2.11 (0.43), residues: 133 sheet: -0.43 (0.28), residues: 369 loop : -2.23 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 412 HIS 0.005 0.001 HIS B 10 PHE 0.013 0.002 PHE F 497 TYR 0.009 0.001 TYR F 367 ARG 0.004 0.000 ARG E 875 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: F 11 MET cc_start: 0.8515 (mmm) cc_final: 0.8304 (mmt) REVERT: F 97 GLU cc_start: 0.8099 (tp30) cc_final: 0.7579 (tm-30) REVERT: F 504 MET cc_start: 0.8196 (mmm) cc_final: 0.7959 (mmm) REVERT: E 98 MET cc_start: 0.8944 (mmt) cc_final: 0.8706 (mmt) REVERT: E 504 MET cc_start: 0.8465 (mtm) cc_final: 0.8252 (mtm) REVERT: E 831 MET cc_start: 0.8123 (ppp) cc_final: 0.7895 (ppp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2448 time to fit residues: 46.2241 Evaluate side-chains 73 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 146 optimal weight: 0.0040 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 829 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14469 Z= 0.169 Angle : 0.812 12.992 19727 Z= 0.423 Chirality : 0.048 0.391 2107 Planarity : 0.006 0.115 2474 Dihedral : 15.845 161.282 2123 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.13 % Allowed : 0.99 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.35 (0.20), residues: 1658 helix: -1.92 (0.43), residues: 127 sheet: -0.38 (0.27), residues: 375 loop : -2.07 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 412 HIS 0.007 0.001 HIS B 10 PHE 0.013 0.001 PHE F 89 TYR 0.009 0.001 TYR F 367 ARG 0.004 0.000 ARG E 873 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: F 97 GLU cc_start: 0.7912 (tp30) cc_final: 0.7500 (tm-30) REVERT: F 504 MET cc_start: 0.8191 (mmm) cc_final: 0.7941 (mmm) REVERT: E 294 MET cc_start: 0.7844 (tmm) cc_final: 0.7451 (tmm) REVERT: E 442 MET cc_start: 0.8964 (tpt) cc_final: 0.8436 (tpt) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2281 time to fit residues: 43.3929 Evaluate side-chains 71 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.0970 chunk 140 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 90 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 117 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 135 optimal weight: 0.0980 chunk 141 optimal weight: 0.9990 chunk 98 optimal weight: 0.0060 chunk 158 optimal weight: 5.9990 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 ASN F 199 HIS ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 829 HIS F 865 HIS E 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14469 Z= 0.142 Angle : 0.806 13.092 19727 Z= 0.420 Chirality : 0.047 0.339 2107 Planarity : 0.006 0.113 2474 Dihedral : 15.640 162.428 2123 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.14 (0.20), residues: 1658 helix: -1.71 (0.45), residues: 120 sheet: -0.25 (0.28), residues: 368 loop : -1.92 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 632 HIS 0.004 0.001 HIS F 185 PHE 0.018 0.001 PHE F 759 TYR 0.008 0.001 TYR F 401 ARG 0.004 0.000 ARG E 873 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 98 MET cc_start: 0.7844 (ttp) cc_final: 0.7445 (ttp) REVERT: F 497 PHE cc_start: 0.8480 (p90) cc_final: 0.8262 (p90) REVERT: F 504 MET cc_start: 0.8040 (mmm) cc_final: 0.7792 (mmm) REVERT: E 294 MET cc_start: 0.7646 (tmm) cc_final: 0.7368 (tmm) REVERT: E 442 MET cc_start: 0.8854 (tpt) cc_final: 0.8146 (tpt) REVERT: E 614 LYS cc_start: 0.8712 (mppt) cc_final: 0.8459 (tptp) REVERT: E 831 MET cc_start: 0.8044 (ppp) cc_final: 0.7677 (tpt) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.2277 time to fit residues: 44.6220 Evaluate side-chains 81 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 548 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14469 Z= 0.268 Angle : 0.840 13.114 19727 Z= 0.436 Chirality : 0.049 0.343 2107 Planarity : 0.006 0.118 2474 Dihedral : 15.803 163.154 2123 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.20 % Allowed : 0.26 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.28 (0.20), residues: 1658 helix: -1.89 (0.42), residues: 139 sheet: -0.46 (0.27), residues: 382 loop : -1.97 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 412 HIS 0.005 0.001 HIS B 10 PHE 0.021 0.002 PHE E 428 TYR 0.012 0.001 TYR E 91 ARG 0.007 0.001 ARG F 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 504 MET cc_start: 0.8378 (mmm) cc_final: 0.7863 (mmm) REVERT: F 593 THR cc_start: 0.6743 (m) cc_final: 0.5860 (t) REVERT: E 442 MET cc_start: 0.8851 (tpt) cc_final: 0.8420 (tpt) REVERT: E 614 LYS cc_start: 0.8779 (mppt) cc_final: 0.8477 (tptp) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.2341 time to fit residues: 41.1887 Evaluate side-chains 77 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 55 optimal weight: 0.0370 chunk 136 optimal weight: 0.0050 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 ASN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.138607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106697 restraints weight = 73986.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100697 restraints weight = 68143.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097808 restraints weight = 42848.675| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14469 Z= 0.148 Angle : 0.809 13.149 19727 Z= 0.421 Chirality : 0.047 0.329 2107 Planarity : 0.006 0.114 2474 Dihedral : 15.651 162.644 2123 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.13 % Allowed : 0.33 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.25 % Twisted Proline : 1.16 % 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: -2.13 (0.20), residues: 1658 helix: -1.61 (0.46), residues: 120 sheet: -0.29 (0.28), residues: 375 loop : -1.91 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 412 HIS 0.007 0.001 HIS F 187 PHE 0.020 0.001 PHE F 759 TYR 0.010 0.001 TYR E 67 ARG 0.004 0.000 ARG E 873 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.40 seconds wall clock time: 57 minutes 8.31 seconds (3428.31 seconds total)