Starting phenix.real_space_refine (version: dev) on Wed Feb 22 20:27:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2023/7r1f_14240_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18372 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5776 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 26, 'TRANS': 693} Chain: "B" Number of atoms: 5762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 728, 5715 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 693} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 728, 5715 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 693} Chain breaks: 2 bond proxies already assigned to first conformer: 5777 Chain: "C" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5836 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Chain: "V" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "R" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 468 Unusual residues: {'GTA': 1, 'K1F': 2} Classifications: {'RNA': 18, 'undetermined': 3} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 16, None: 3} Not linked: pdbres="GTA M 1 " pdbres=" A M 2 " Not linked: pdbres=" C M 19 " pdbres="K1F M 20 " Not linked: pdbres="K1F M 20 " pdbres="K1F M 21 " Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG B 239 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 239 " occ=0.50 residue: pdb=" N AMET B 408 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 408 " occ=0.50 residue: pdb=" N AMET B 409 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 409 " occ=0.50 residue: pdb=" N AMET B 410 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 410 " occ=0.50 residue: pdb=" N AGLY B 411 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 411 " occ=0.50 residue: pdb=" N AMET B 412 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 412 " occ=0.50 Time building chain proxies: 12.70, per 1000 atoms: 0.69 Number of scatterers: 18372 At special positions: 0 Unit cell: (120.834, 124.122, 120.834, 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 136 16.00 P 47 15.00 Mg 3 11.99 O 3567 8.00 N 3161 7.00 C 11458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 21 sheets defined 44.1% alpha, 11.3% beta 11 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 128 through 139 removed outlier: 4.347A pdb=" N LYS A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 333 through 348 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 430 through 448 removed outlier: 3.765A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 4.051A pdb=" N GLN A 579 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 582 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 586 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 629 through 645 Processing helix chain 'A' and resid 649 through 669 Processing helix chain 'A' and resid 679 through 689 removed outlier: 4.219A pdb=" N CYS A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 716 removed outlier: 4.270A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.933A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.531A pdb=" N LYS B 160 " --> pdb=" O GLY B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.850A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.328A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.273A pdb=" N ALA B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 505 through 511 Proline residue: B 509 - end of helix Processing helix chain 'B' and resid 518 through 535 removed outlier: 3.607A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 558 Processing helix chain 'B' and resid 570 through 581 removed outlier: 4.334A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 607 through 610 No H-bonds generated for 'chain 'B' and resid 607 through 610' Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 681 through 698 Processing helix chain 'B' and resid 713 through 730 Processing helix chain 'B' and resid 736 through 748 Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.769A pdb=" N ARG C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 27 through 35 removed outlier: 4.318A pdb=" N ASN C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 removed outlier: 4.058A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 113 through 116 No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.728A pdb=" N ILE C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 228 through 237 removed outlier: 4.262A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N HIS C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 274 removed outlier: 4.331A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.686A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 432 through 442 removed outlier: 4.238A pdb=" N ASN C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 537 through 540 Processing helix chain 'C' and resid 543 through 556 Processing helix chain 'C' and resid 558 through 567 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.813A pdb=" N SER C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.863A pdb=" N GLY C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLN C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 Processing helix chain 'C' and resid 683 through 687 Processing helix chain 'C' and resid 691 through 693 No H-bonds generated for 'chain 'C' and resid 691 through 693' Processing helix chain 'C' and resid 714 through 717 No H-bonds generated for 'chain 'C' and resid 714 through 717' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= C, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.291A pdb=" N MET A 146 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR A 124 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 148 " --> pdb=" O THR A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.502A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 498 through 502 removed outlier: 6.409A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 614 through 619 removed outlier: 7.026A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= H, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= I, first strand: chain 'B' and resid 178 through 191 Processing sheet with id= J, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.576A pdb=" N ILE B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 226 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 482 through 485 Processing sheet with id= L, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= M, first strand: chain 'B' and resid 488 through 491 Processing sheet with id= N, first strand: chain 'C' and resid 135 through 137 Processing sheet with id= O, first strand: chain 'C' and resid 143 through 148 Processing sheet with id= P, first strand: chain 'C' and resid 289 through 291 Processing sheet with id= Q, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.118A pdb=" N GLU C 364 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 341 through 347 Processing sheet with id= S, first strand: chain 'C' and resid 639 through 641 Processing sheet with id= T, first strand: chain 'C' and resid 659 through 662 Processing sheet with id= U, first strand: chain 'C' and resid 725 through 729 removed outlier: 3.724A pdb=" N GLY C 702 " --> pdb=" O LYS C 737 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL C 700 " --> pdb=" O VAL C 739 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4695 1.33 - 1.45: 3491 1.45 - 1.57: 10297 1.57 - 1.69: 89 1.69 - 1.81: 232 Bond restraints: 18804 Sorted by residual: bond pdb=" C3B GTA M 1 " pdb=" C4B GTA M 1 " ideal model delta sigma weight residual 1.275 1.516 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B GTA M 1 " pdb=" C2B GTA M 1 " ideal model delta sigma weight residual 1.277 1.508 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C18 K1F M 21 " pdb=" C20 K1F M 21 " ideal model delta sigma weight residual 1.315 1.521 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C18 K1F M 20 " pdb=" C20 K1F M 20 " ideal model delta sigma weight residual 1.315 1.520 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C5 GTA M 1 " pdb=" C6 GTA M 1 " ideal model delta sigma weight residual 1.541 1.336 0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 18799 not shown) Histogram of bond angle deviations from ideal: 94.01 - 102.01: 149 102.01 - 110.02: 3053 110.02 - 118.02: 11300 118.02 - 126.02: 10653 126.02 - 134.02: 390 Bond angle restraints: 25545 Sorted by residual: angle pdb=" C5C GTA M 1 " pdb=" C6C GTA M 1 " pdb=" N6C GTA M 1 " ideal model delta sigma weight residual 130.29 116.29 14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" N1C GTA M 1 " pdb=" C6C GTA M 1 " pdb=" N6C GTA M 1 " ideal model delta sigma weight residual 109.68 121.97 -12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C1A GTA M 1 " pdb=" C2A GTA M 1 " pdb=" C3A GTA M 1 " ideal model delta sigma weight residual 105.72 94.01 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C1A GTA M 1 " pdb=" N9 GTA M 1 " pdb=" C4 GTA M 1 " ideal model delta sigma weight residual 114.98 125.46 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O21 GTA M 1 " pdb=" P2 GTA M 1 " pdb=" O22 GTA M 1 " ideal model delta sigma weight residual 109.44 119.65 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 25540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 11102 27.83 - 55.66: 269 55.66 - 83.49: 27 83.49 - 111.32: 3 111.32 - 139.14: 1 Dihedral angle restraints: 11402 sinusoidal: 5093 harmonic: 6309 Sorted by residual: dihedral pdb=" O4' C M 4 " pdb=" C1' C M 4 " pdb=" N1 C M 4 " pdb=" C2 C M 4 " ideal model delta sinusoidal sigma weight residual -160.00 -110.81 -49.19 1 1.50e+01 4.44e-03 1.48e+01 dihedral pdb=" CA ARG B 350 " pdb=" C ARG B 350 " pdb=" N LEU B 351 " pdb=" CA LEU B 351 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" P U M 18 " pdb=" O5' U M 18 " pdb=" C5' U M 18 " pdb=" C4' U M 18 " ideal model delta sinusoidal sigma weight residual 170.00 -50.86 -139.14 1 4.00e+01 6.25e-04 1.05e+01 ... (remaining 11399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2572 0.068 - 0.137: 251 0.137 - 0.205: 5 0.205 - 0.273: 0 0.273 - 0.342: 5 Chirality restraints: 2833 Sorted by residual: chirality pdb=" C4B GTA M 1 " pdb=" C3B GTA M 1 " pdb=" C5B GTA M 1 " pdb=" O4B GTA M 1 " both_signs ideal model delta sigma weight residual False -2.46 -2.81 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C3A GTA M 1 " pdb=" C2A GTA M 1 " pdb=" C4A GTA M 1 " pdb=" O3A GTA M 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.79 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3B GTA M 1 " pdb=" C2B GTA M 1 " pdb=" C4B GTA M 1 " pdb=" O3B GTA M 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.79 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2830 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 176 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO C 177 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 582 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C GLN A 582 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN A 582 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 583 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 533 " 0.025 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 534 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.021 5.00e-02 4.00e+02 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 188 2.61 - 3.18: 15697 3.18 - 3.75: 29634 3.75 - 4.33: 42657 4.33 - 4.90: 68272 Nonbonded interactions: 156448 Sorted by model distance: nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 803 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 802 " model vdw 2.041 2.170 nonbonded pdb=" OD1 ASN B 310 " pdb=" O2' C M 17 " model vdw 2.107 2.440 nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.114 2.440 nonbonded pdb=" NH1 ARG B 45 " pdb=" OE2 GLU B 311 " model vdw 2.220 2.520 ... (remaining 156443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 3 5.21 5 S 136 5.16 5 C 11458 2.51 5 N 3161 2.21 5 O 3567 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.680 Check model and map are aligned: 0.250 Process input model: 53.790 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.008 0.241 18804 Z= 0.485 Angle : 0.587 13.998 25545 Z= 0.289 Chirality : 0.043 0.342 2833 Planarity : 0.004 0.045 3114 Dihedral : 12.132 139.144 7338 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.37 (0.18), residues: 2175 helix: 1.25 (0.17), residues: 972 sheet: -0.15 (0.33), residues: 244 loop : -0.63 (0.19), residues: 959 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 14 residues processed: 259 average time/residue: 1.6822 time to fit residues: 479.4145 Evaluate side-chains 165 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 2.9178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.0870 chunk 128 optimal weight: 4.9990 chunk 199 optimal weight: 0.4980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS B 124 GLN B 276 ASN ** B 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 18804 Z= 0.174 Angle : 0.540 8.380 25545 Z= 0.271 Chirality : 0.039 0.234 2833 Planarity : 0.004 0.045 3114 Dihedral : 7.005 139.362 2920 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.50 (0.18), residues: 2175 helix: 1.46 (0.17), residues: 975 sheet: -0.18 (0.34), residues: 235 loop : -0.67 (0.19), residues: 965 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 183 average time/residue: 1.5150 time to fit residues: 308.6191 Evaluate side-chains 152 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 2 average time/residue: 0.7809 time to fit residues: 4.7541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 166 optimal weight: 0.0010 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 160 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 675 ASN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18804 Z= 0.186 Angle : 0.524 8.405 25545 Z= 0.260 Chirality : 0.039 0.160 2833 Planarity : 0.004 0.045 3114 Dihedral : 6.858 138.619 2920 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.37 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.61 (0.18), residues: 2175 helix: 1.57 (0.17), residues: 976 sheet: -0.14 (0.34), residues: 233 loop : -0.63 (0.19), residues: 966 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 175 average time/residue: 1.5336 time to fit residues: 300.4608 Evaluate side-chains 149 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 2.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 1.9990 chunk 150 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 18804 Z= 0.155 Angle : 0.513 12.063 25545 Z= 0.251 Chirality : 0.038 0.160 2833 Planarity : 0.003 0.041 3114 Dihedral : 6.755 137.974 2920 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.37 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.68 (0.18), residues: 2175 helix: 1.68 (0.17), residues: 971 sheet: -0.16 (0.34), residues: 233 loop : -0.63 (0.19), residues: 971 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 176 average time/residue: 1.4500 time to fit residues: 285.8897 Evaluate side-chains 159 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 1.0134 time to fit residues: 6.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 18804 Z= 0.276 Angle : 0.550 10.604 25545 Z= 0.271 Chirality : 0.040 0.216 2833 Planarity : 0.004 0.066 3114 Dihedral : 6.817 141.629 2920 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.70 (0.18), residues: 2175 helix: 1.70 (0.17), residues: 967 sheet: -0.25 (0.34), residues: 235 loop : -0.59 (0.19), residues: 973 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 2.097 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: symmetry clash outliers start: 45 outliers final: 22 residues processed: 178 average time/residue: 1.5387 time to fit residues: 306.8447 Evaluate side-chains 156 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.3184 time to fit residues: 4.5928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.0370 chunk 191 optimal weight: 10.0000 chunk 42 optimal weight: 0.0060 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18804 Z= 0.181 Angle : 0.533 11.141 25545 Z= 0.258 Chirality : 0.038 0.212 2833 Planarity : 0.003 0.040 3114 Dihedral : 6.770 140.764 2920 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.23 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.73 (0.18), residues: 2175 helix: 1.73 (0.17), residues: 971 sheet: -0.36 (0.34), residues: 228 loop : -0.55 (0.19), residues: 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 2.023 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: symmetry clash outliers start: 37 outliers final: 23 residues processed: 170 average time/residue: 1.5094 time to fit residues: 286.7401 Evaluate side-chains 158 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 1.3469 time to fit residues: 7.5251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 179 optimal weight: 0.0470 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 0.0870 chunk 132 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 18804 Z= 0.150 Angle : 0.546 11.268 25545 Z= 0.261 Chirality : 0.038 0.186 2833 Planarity : 0.003 0.047 3114 Dihedral : 6.692 138.312 2920 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.37 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.18), residues: 2175 helix: 1.78 (0.17), residues: 969 sheet: -0.32 (0.35), residues: 226 loop : -0.51 (0.19), residues: 980 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 2.125 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: symmetry clash outliers start: 33 outliers final: 20 residues processed: 170 average time/residue: 1.5538 time to fit residues: 296.1173 Evaluate side-chains 152 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 2.143 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.4145 time to fit residues: 3.5046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 192 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 18804 Z= 0.177 Angle : 0.558 12.370 25545 Z= 0.265 Chirality : 0.038 0.203 2833 Planarity : 0.003 0.053 3114 Dihedral : 6.650 137.741 2920 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 97.00 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.77 (0.18), residues: 2175 helix: 1.72 (0.17), residues: 974 sheet: -0.30 (0.35), residues: 226 loop : -0.49 (0.19), residues: 975 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 2.144 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: symmetry clash outliers start: 34 outliers final: 24 residues processed: 165 average time/residue: 1.5744 time to fit residues: 290.1037 Evaluate side-chains 157 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.3358 time to fit residues: 4.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 186 optimal weight: 0.0060 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 18804 Z= 0.201 Angle : 0.575 11.901 25545 Z= 0.275 Chirality : 0.039 0.199 2833 Planarity : 0.003 0.053 3114 Dihedral : 6.657 138.347 2920 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.76 (0.18), residues: 2175 helix: 1.72 (0.17), residues: 970 sheet: -0.31 (0.34), residues: 226 loop : -0.49 (0.19), residues: 979 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.263 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: symmetry clash outliers start: 29 outliers final: 25 residues processed: 159 average time/residue: 1.5495 time to fit residues: 274.6131 Evaluate side-chains 153 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.3115 time to fit residues: 3.8719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 145 optimal weight: 0.0070 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 134 optimal weight: 0.0030 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 18804 Z= 0.151 Angle : 0.584 13.761 25545 Z= 0.276 Chirality : 0.038 0.177 2833 Planarity : 0.003 0.053 3114 Dihedral : 6.592 135.869 2920 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.82 (0.18), residues: 2175 helix: 1.78 (0.17), residues: 965 sheet: -0.28 (0.34), residues: 227 loop : -0.47 (0.19), residues: 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 1.5620 time to fit residues: 271.3750 Evaluate side-chains 155 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 1.6856 time to fit residues: 8.6131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 53 optimal weight: 0.0370 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 73 optimal weight: 0.0060 chunk 179 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.070715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050455 restraints weight = 105006.527| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.11 r_work: 0.2815 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 18804 Z= 0.190 Angle : 0.598 12.807 25545 Z= 0.283 Chirality : 0.038 0.189 2833 Planarity : 0.004 0.053 3114 Dihedral : 6.576 135.970 2920 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.18), residues: 2175 helix: 1.75 (0.17), residues: 969 sheet: -0.34 (0.34), residues: 231 loop : -0.47 (0.19), residues: 975 =============================================================================== Job complete usr+sys time: 5991.84 seconds wall clock time: 107 minutes 42.90 seconds (6462.90 seconds total)