Starting phenix.real_space_refine on Wed Nov 15 06:38:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yq4_34019/11_2023/7yq4_34019_updated.pdb" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 90 5.16 5 C 6655 2.51 5 N 1831 2.21 5 O 2012 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "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 698": "OE1" <-> "OE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 717": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10618 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 583, 4701 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 553} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 583, 4701 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 553} Chain breaks: 1 bond proxies already assigned to first conformer: 4806 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: "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: "F" Number of atoms: 4958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4958 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 580} Chain breaks: 2 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 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: 8.25, per 1000 atoms: 0.78 Number of scatterers: 10618 At special positions: 0 Unit cell: (90.95, 139.4, 141.95, 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 90 16.00 P 24 15.00 F 6 9.00 O 2012 8.00 N 1831 7.00 C 6655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS A 20 " distance=2.01 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 2.5 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 15 sheets defined 9.8% alpha, 10.5% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... 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 '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 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' 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 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 sheet with id= A, first strand: chain 'E' and resid 11 through 14 Processing sheet with id= B, 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= C, first strand: chain 'E' and resid 278 through 280 Processing sheet with id= D, 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= D Processing sheet with id= E, 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= E Processing sheet with id= F, 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= F Processing sheet with id= G, 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= H, 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= I, first strand: chain 'F' and resid 231 through 233 Processing sheet with id= J, 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= K, 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= L, 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= M, first strand: chain 'F' and resid 400 through 402 Processing sheet with id= N, 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= O, 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) 93 hydrogen bonds defined for protein. 237 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: 2.34 Time building geometry restraints manager: 4.69 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: 1716 1.31 - 1.44: 3126 1.44 - 1.58: 5914 1.58 - 1.71: 57 1.71 - 1.84: 116 Bond restraints: 10929 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 10924 not shown) Histogram of bond angle deviations from ideal: 96.91 - 105.62: 326 105.62 - 114.34: 6198 114.34 - 123.05: 7436 123.05 - 131.76: 916 131.76 - 140.48: 35 Bond angle restraints: 14911 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=" C1' OMG G 11 " pdb=" N9 OMG G 11 " pdb=" C4 OMG G 11 " ideal model delta sigma weight residual 108.29 123.87 -15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C LEU E 315 " pdb=" N GLU E 316 " pdb=" CA GLU E 316 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 ... (remaining 14906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 6251 34.89 - 69.78: 251 69.78 - 104.68: 35 104.68 - 139.57: 1 139.57 - 174.46: 6 Dihedral angle restraints: 6544 sinusoidal: 2911 harmonic: 3633 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 6541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1299 0.083 - 0.167: 252 0.167 - 0.250: 26 0.250 - 0.334: 5 0.334 - 0.417: 5 Chirality restraints: 1587 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 1584 not shown) Planarity restraints: 1845 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 1842 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2326 2.78 - 3.31: 8726 3.31 - 3.84: 16220 3.84 - 4.37: 17819 4.37 - 4.90: 30834 Nonbonded interactions: 75925 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=" N3 DUZ G 14 " pdb=" O21 85Y G 16 " model vdw 2.316 2.520 nonbonded pdb=" OD1 ASP E 499 " pdb=" OG1 THR E 571 " model vdw 2.325 2.440 ... (remaining 75920 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 591)) selection = (chain 'F' and (resid 4 through 143 or resid 145 through 160 or resid 169 throug \ h 591)) } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 15.630 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 35.370 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.016 0.297 10929 Z= 0.890 Angle : 1.302 21.004 14911 Z= 0.635 Chirality : 0.069 0.417 1587 Planarity : 0.021 0.547 1845 Dihedral : 18.740 174.460 4094 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.53 % Allowed : 9.24 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -4.40 (0.19), residues: 1232 helix: -5.00 (0.15), residues: 108 sheet: -2.14 (0.35), residues: 188 loop : -3.09 (0.17), residues: 936 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 183 average time/residue: 0.2843 time to fit residues: 69.0842 Evaluate side-chains 96 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0930 time to fit residues: 1.8697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN F 148 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS F 263 HIS F 268 ASN F 429 HIS F 541 ASN F 589 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10929 Z= 0.213 Angle : 0.946 16.054 14911 Z= 0.489 Chirality : 0.050 0.420 1587 Planarity : 0.007 0.122 1845 Dihedral : 18.611 164.280 1635 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.38 % Allowed : 17.17 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -3.82 (0.20), residues: 1232 helix: -3.85 (0.29), residues: 110 sheet: -1.49 (0.38), residues: 190 loop : -2.84 (0.17), residues: 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 0.2035 time to fit residues: 39.8743 Evaluate side-chains 104 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0987 time to fit residues: 4.0686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 31 optimal weight: 0.0570 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN E 108 ASN E 122 ASN B 3 ASN F 122 ASN F 144 HIS ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS F 407 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10929 Z= 0.158 Angle : 0.879 15.115 14911 Z= 0.460 Chirality : 0.048 0.360 1587 Planarity : 0.006 0.117 1845 Dihedral : 18.059 163.084 1635 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.46 % Allowed : 19.98 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -3.41 (0.21), residues: 1232 helix: -2.97 (0.40), residues: 110 sheet: -1.07 (0.39), residues: 180 loop : -2.65 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 138 average time/residue: 0.2151 time to fit residues: 43.2848 Evaluate side-chains 108 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0949 time to fit residues: 3.6074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 0.0030 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 452 GLN B 3 ASN A 15 GLN F 122 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10929 Z= 0.165 Angle : 0.876 13.930 14911 Z= 0.458 Chirality : 0.047 0.347 1587 Planarity : 0.006 0.115 1845 Dihedral : 17.792 164.489 1635 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.64 % Allowed : 19.98 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.22), residues: 1232 helix: -2.46 (0.45), residues: 110 sheet: -0.96 (0.38), residues: 202 loop : -2.45 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 120 average time/residue: 0.2333 time to fit residues: 39.9622 Evaluate side-chains 107 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1433 time to fit residues: 5.2118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN A 15 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN F 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10929 Z= 0.488 Angle : 1.057 13.944 14911 Z= 0.544 Chirality : 0.055 0.377 1587 Planarity : 0.007 0.121 1845 Dihedral : 18.129 166.784 1635 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.11 % Allowed : 22.01 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -3.32 (0.21), residues: 1232 helix: -2.13 (0.46), residues: 112 sheet: -0.70 (0.42), residues: 165 loop : -2.74 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 112 average time/residue: 0.2249 time to fit residues: 37.0676 Evaluate side-chains 97 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0993 time to fit residues: 3.3319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10929 Z= 0.244 Angle : 0.917 13.571 14911 Z= 0.478 Chirality : 0.049 0.366 1587 Planarity : 0.006 0.116 1845 Dihedral : 17.862 163.343 1635 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.58 % Allowed : 22.98 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -3.17 (0.21), residues: 1232 helix: -1.90 (0.46), residues: 116 sheet: -0.68 (0.41), residues: 165 loop : -2.64 (0.18), residues: 951 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 0.2293 time to fit residues: 37.3633 Evaluate side-chains 104 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1000 time to fit residues: 3.2689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 75 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 HIS B 3 ASN F 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10929 Z= 0.176 Angle : 0.877 13.218 14911 Z= 0.459 Chirality : 0.047 0.349 1587 Planarity : 0.006 0.115 1845 Dihedral : 17.619 164.192 1635 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.14 % Allowed : 23.86 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -2.93 (0.22), residues: 1232 helix: -1.57 (0.49), residues: 115 sheet: -0.55 (0.40), residues: 171 loop : -2.49 (0.18), residues: 946 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 112 average time/residue: 0.2047 time to fit residues: 34.0719 Evaluate side-chains 104 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0961 time to fit residues: 2.7304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN F 122 ASN F 295 ASN F 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10929 Z= 0.355 Angle : 0.966 13.082 14911 Z= 0.500 Chirality : 0.051 0.356 1587 Planarity : 0.007 0.118 1845 Dihedral : 17.780 164.373 1635 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 1.85 % Allowed : 23.86 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.22), residues: 1232 helix: -1.53 (0.49), residues: 113 sheet: -0.67 (0.40), residues: 171 loop : -2.62 (0.18), residues: 948 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 109 average time/residue: 0.2079 time to fit residues: 33.5872 Evaluate side-chains 93 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0957 time to fit residues: 2.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN F 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10929 Z= 0.231 Angle : 0.913 13.159 14911 Z= 0.473 Chirality : 0.049 0.339 1587 Planarity : 0.006 0.116 1845 Dihedral : 17.683 164.384 1635 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.14 % Allowed : 24.82 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -2.98 (0.22), residues: 1232 helix: -1.40 (0.50), residues: 113 sheet: -0.73 (0.41), residues: 166 loop : -2.51 (0.18), residues: 953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 103 average time/residue: 0.2129 time to fit residues: 33.0983 Evaluate side-chains 95 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1080 time to fit residues: 2.9595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 417 HIS B 3 ASN F 295 ASN F 429 HIS F 589 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10929 Z= 0.322 Angle : 0.953 13.047 14911 Z= 0.493 Chirality : 0.051 0.336 1587 Planarity : 0.007 0.118 1845 Dihedral : 17.718 164.548 1635 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.62 % Allowed : 24.91 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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 (0.22), residues: 1232 helix: -1.54 (0.49), residues: 114 sheet: -0.80 (0.41), residues: 166 loop : -2.57 (0.18), residues: 952 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 98 average time/residue: 0.2479 time to fit residues: 35.2609 Evaluate side-chains 92 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1012 time to fit residues: 2.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.0060 chunk 91 optimal weight: 0.0030 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN F 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.207094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166995 restraints weight = 44118.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166675 restraints weight = 32950.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164593 restraints weight = 14269.461| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10929 Z= 0.169 Angle : 0.885 13.071 14911 Z= 0.461 Chirality : 0.048 0.318 1587 Planarity : 0.006 0.114 1845 Dihedral : 17.540 165.999 1635 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.44 % Allowed : 25.18 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.34 % Twisted Proline : 1.75 % 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: -2.82 (0.22), residues: 1232 helix: -1.05 (0.53), residues: 107 sheet: -0.80 (0.41), residues: 178 loop : -2.40 (0.18), residues: 947 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.61 seconds wall clock time: 43 minutes 57.91 seconds (2637.91 seconds total)