Starting phenix.real_space_refine on Sat Feb 17 10:26:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_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_2024/7r1f_14240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1f_14240/02_2024/7r1f_14240_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18372 Number of models: 1 Model: "" Number of chains: 11 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: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 417 Classifications: {'RNA': 20} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 17} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 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: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} 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: 12.68, 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.45 Conformation dependent library (CDL) restraints added in 4.1 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: 9.81 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: 6.72 Time building geometry restraints manager: 8.90 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: 91 1.69 - 1.81: 232 Bond restraints: 18806 Sorted by residual: bond pdb=" C06 K1F M 21 " pdb=" C07 K1F M 21 " ideal model delta sigma weight residual 1.708 1.386 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C06 K1F M 20 " pdb=" C07 K1F M 20 " ideal model delta sigma weight residual 1.708 1.388 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C3B GTA M 101 " pdb=" C4B GTA M 101 " 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 101 " pdb=" C2B GTA M 101 " ideal model delta sigma weight residual 1.277 1.508 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C5 GTA M 101 " pdb=" C6 GTA M 101 " ideal model delta sigma weight residual 1.541 1.336 0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 18801 not shown) Histogram of bond angle deviations from ideal: 94.01 - 102.01: 149 102.01 - 110.02: 3057 110.02 - 118.02: 11300 118.02 - 126.02: 10655 126.02 - 134.02: 390 Bond angle restraints: 25551 Sorted by residual: angle pdb=" C5C GTA M 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " 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 101 " pdb=" C6C GTA M 101 " pdb=" N6C GTA M 101 " 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 101 " pdb=" C2A GTA M 101 " pdb=" C3A GTA M 101 " 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 101 " pdb=" N9 GTA M 101 " pdb=" C4 GTA M 101 " 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 101 " pdb=" P2 GTA M 101 " pdb=" O22 GTA M 101 " ideal model delta sigma weight residual 109.44 119.65 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 25546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.83: 11103 27.83 - 55.66: 322 55.66 - 83.49: 65 83.49 - 111.32: 3 111.32 - 139.14: 1 Dihedral angle restraints: 11494 sinusoidal: 5185 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 11491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2674 0.082 - 0.164: 158 0.164 - 0.246: 2 0.246 - 0.328: 4 0.328 - 0.410: 3 Chirality restraints: 2841 Sorted by residual: chirality pdb=" C3' K1F M 20 " pdb=" C4' K1F M 20 " pdb=" O3' K1F M 20 " pdb=" C2' K1F M 20 " both_signs ideal model delta sigma weight residual False -2.42 -2.83 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C3' K1F M 21 " pdb=" C4' K1F M 21 " pdb=" O3' K1F M 21 " pdb=" C2' K1F M 21 " both_signs ideal model delta sigma weight residual False -2.42 -2.81 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C4B GTA M 101 " pdb=" C3B GTA M 101 " pdb=" C5B GTA M 101 " pdb=" O4B GTA M 101 " both_signs ideal model delta sigma weight residual False -2.46 -2.81 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2838 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 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: 5.680 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: 18.770 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 61.900 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.009 0.322 18806 Z= 0.521 Angle : 0.615 13.998 25551 Z= 0.295 Chirality : 0.044 0.410 2841 Planarity : 0.004 0.045 3114 Dihedral : 13.370 139.144 7430 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 % Allowed : 5.77 % Favored : 91.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 437 HIS 0.003 0.001 HIS B 561 PHE 0.012 0.001 PHE B 550 TYR 0.019 0.002 TYR C 207 ARG 0.004 0.000 ARG B 45 *********************** 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 : 2.165 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: A 44 VAL cc_start: 0.8995 (m) cc_final: 0.8725 (p) outliers start: 44 outliers final: 14 residues processed: 259 average time/residue: 1.6387 time to fit residues: 466.1492 Evaluate side-chains 166 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 694 VAL 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: 0.8195 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18806 Z= 0.176 Angle : 0.567 11.752 25551 Z= 0.277 Chirality : 0.039 0.225 2841 Planarity : 0.004 0.044 3114 Dihedral : 11.422 139.629 3034 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 1.99 % Allowed : 11.80 % Favored : 86.21 % 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: 0.51 (0.18), residues: 2175 helix: 1.46 (0.17), residues: 975 sheet: -0.17 (0.34), residues: 235 loop : -0.67 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 182 HIS 0.004 0.001 HIS C 366 PHE 0.017 0.001 PHE A 132 TYR 0.020 0.001 TYR C 704 ARG 0.009 0.000 ARG C 69 *********************** 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 190 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 2.359 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 REVERT: A 347 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8435 (tt) REVERT: B 654 MET cc_start: 0.7292 (pp-130) cc_final: 0.7063 (pp-130) REVERT: C 329 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7668 (mtm180) REVERT: C 404 MET cc_start: 0.8846 (ptm) cc_final: 0.8643 (ptp) REVERT: C 409 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6363 (p0) outliers start: 38 outliers final: 16 residues processed: 182 average time/residue: 1.5312 time to fit residues: 311.7008 Evaluate side-chains 154 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL 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: 0.3980 chunk 166 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 675 ASN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18806 Z= 0.164 Angle : 0.545 12.201 25551 Z= 0.263 Chirality : 0.039 0.222 2841 Planarity : 0.004 0.044 3114 Dihedral : 11.291 138.182 3030 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 1.99 % Allowed : 12.06 % Favored : 85.95 % 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: 0.63 (0.18), residues: 2175 helix: 1.58 (0.17), residues: 977 sheet: -0.12 (0.34), residues: 233 loop : -0.63 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 182 HIS 0.007 0.001 HIS C 366 PHE 0.014 0.001 PHE A 24 TYR 0.016 0.001 TYR C 704 ARG 0.009 0.000 ARG A 608 *********************** 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 184 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8461 (tt) REVERT: C 409 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6524 (p0) outliers start: 38 outliers final: 18 residues processed: 176 average time/residue: 1.4642 time to fit residues: 286.6866 Evaluate side-chains 152 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18806 Z= 0.187 Angle : 0.547 12.318 25551 Z= 0.261 Chirality : 0.039 0.181 2841 Planarity : 0.004 0.046 3114 Dihedral : 11.206 138.820 3026 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 1.63 % Allowed : 13.27 % Favored : 85.11 % 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: 0.66 (0.18), residues: 2175 helix: 1.62 (0.17), residues: 975 sheet: -0.14 (0.35), residues: 233 loop : -0.62 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 182 HIS 0.002 0.001 HIS B 47 PHE 0.012 0.001 PHE A 132 TYR 0.015 0.001 TYR C 704 ARG 0.007 0.000 ARG C 14 *********************** 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 177 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.7536 (pmm) cc_final: 0.7218 (pmt) REVERT: A 347 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8443 (tt) REVERT: B 115 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6751 (mmm) REVERT: C 404 MET cc_start: 0.8811 (ptm) cc_final: 0.8584 (ptp) REVERT: C 409 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6603 (p0) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 1.4819 time to fit residues: 279.8393 Evaluate side-chains 159 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 0.0270 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.3644 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18806 Z= 0.250 Angle : 0.567 12.251 25551 Z= 0.271 Chirality : 0.040 0.179 2841 Planarity : 0.004 0.068 3114 Dihedral : 11.212 141.135 3026 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.14 % Rotamer: Outliers : 2.31 % Allowed : 13.21 % Favored : 84.48 % 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: 1.68 (0.17), residues: 969 sheet: -0.21 (0.35), residues: 223 loop : -0.58 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 344 TYR 0.016 0.001 TYR C 207 ARG 0.014 0.000 ARG A 608 *********************** 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 184 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 2.346 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 REVERT: A 347 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8477 (tt) REVERT: B 115 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6723 (mmm) REVERT: C 396 MET cc_start: 0.7953 (mmt) cc_final: 0.7180 (mpp) REVERT: C 409 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6579 (p0) outliers start: 44 outliers final: 20 residues processed: 174 average time/residue: 1.4669 time to fit residues: 285.5873 Evaluate side-chains 157 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18806 Z= 0.184 Angle : 0.560 12.191 25551 Z= 0.264 Chirality : 0.039 0.184 2841 Planarity : 0.003 0.039 3114 Dihedral : 11.185 140.130 3026 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.99 % Allowed : 13.48 % Favored : 84.53 % 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: 969 sheet: -0.31 (0.35), residues: 228 loop : -0.55 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 182 HIS 0.009 0.001 HIS C 366 PHE 0.021 0.001 PHE A 4 TYR 0.012 0.001 TYR B 554 ARG 0.007 0.000 ARG B 126 *********************** 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 182 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 2.336 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 revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8370 (mmp-170) cc_final: 0.8062 (mmp-170) REVERT: A 347 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8453 (tt) REVERT: C 409 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6515 (p0) outliers start: 38 outliers final: 23 residues processed: 169 average time/residue: 1.5025 time to fit residues: 282.5275 Evaluate side-chains 162 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 179 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18806 Z= 0.171 Angle : 0.570 12.181 25551 Z= 0.268 Chirality : 0.038 0.182 2841 Planarity : 0.004 0.072 3114 Dihedral : 11.147 138.650 3026 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.37 % Rotamer: Outliers : 1.68 % Allowed : 14.42 % Favored : 83.90 % 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: 1.77 (0.17), residues: 967 sheet: -0.31 (0.35), residues: 226 loop : -0.53 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 133 HIS 0.003 0.000 HIS C 366 PHE 0.011 0.001 PHE B 344 TYR 0.012 0.001 TYR B 554 ARG 0.018 0.000 ARG A 608 *********************** 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 173 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 2.450 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 revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8361 (mmp-170) cc_final: 0.8050 (mmt180) REVERT: A 347 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8448 (tt) REVERT: C 396 MET cc_start: 0.8133 (mmt) cc_final: 0.7914 (mmt) REVERT: C 409 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6459 (p0) outliers start: 31 outliers final: 20 residues processed: 166 average time/residue: 1.5332 time to fit residues: 283.1157 Evaluate side-chains 156 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 694 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 B 670 ASN C 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.004 0.048 18806 Z= 0.278 Angle : 0.611 12.254 25551 Z= 0.286 Chirality : 0.040 0.182 2841 Planarity : 0.004 0.047 3114 Dihedral : 11.164 140.819 3024 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.78 % Allowed : 14.58 % Favored : 83.64 % 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: 0.71 (0.18), residues: 2175 helix: 1.70 (0.17), residues: 968 sheet: -0.36 (0.34), residues: 228 loop : -0.55 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 182 HIS 0.003 0.001 HIS B 47 PHE 0.016 0.001 PHE A 4 TYR 0.013 0.001 TYR C 704 ARG 0.008 0.000 ARG C 329 *********************** 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 167 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.028 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: A 51 MET cc_start: 0.7024 (ptt) cc_final: 0.6799 (ppp) REVERT: A 173 ARG cc_start: 0.8325 (mmp-170) cc_final: 0.7925 (mmp-170) REVERT: A 347 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8470 (tt) REVERT: C 396 MET cc_start: 0.8131 (mmt) cc_final: 0.7210 (mpp) REVERT: C 409 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6506 (p0) outliers start: 33 outliers final: 21 residues processed: 158 average time/residue: 1.5760 time to fit residues: 276.7487 Evaluate side-chains 155 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 178 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18806 Z= 0.171 Angle : 0.593 12.353 25551 Z= 0.276 Chirality : 0.038 0.184 2841 Planarity : 0.003 0.052 3114 Dihedral : 11.132 139.010 3023 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 1.57 % Allowed : 15.05 % Favored : 83.38 % 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: 0.75 (0.18), residues: 2175 helix: 1.71 (0.17), residues: 970 sheet: -0.33 (0.34), residues: 226 loop : -0.50 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 182 HIS 0.003 0.000 HIS C 366 PHE 0.012 0.001 PHE A 709 TYR 0.012 0.001 TYR B 554 ARG 0.007 0.000 ARG C 329 *********************** 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 162 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 2.115 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 revert: symmetry clash REVERT: A 51 MET cc_start: 0.7002 (ptt) cc_final: 0.6721 (ppp) REVERT: A 347 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8455 (tt) REVERT: C 396 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7228 (mpp) REVERT: C 409 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6390 (p0) outliers start: 29 outliers final: 22 residues processed: 155 average time/residue: 1.5260 time to fit residues: 264.2592 Evaluate side-chains 156 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 174 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18806 Z= 0.173 Angle : 0.617 13.362 25551 Z= 0.283 Chirality : 0.039 0.191 2841 Planarity : 0.003 0.051 3114 Dihedral : 11.079 137.665 3023 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 1.42 % Allowed : 15.26 % Favored : 83.32 % 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: 0.75 (0.18), residues: 2175 helix: 1.69 (0.17), residues: 971 sheet: -0.36 (0.34), residues: 227 loop : -0.47 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 182 HIS 0.004 0.001 HIS C 366 PHE 0.014 0.001 PHE A 709 TYR 0.012 0.001 TYR B 554 ARG 0.007 0.000 ARG B 126 ********************** 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 157 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 2.174 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: A 173 ARG cc_start: 0.8308 (mmp-170) cc_final: 0.7995 (mmp-170) REVERT: A 347 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8456 (tt) REVERT: C 396 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7240 (mpp) REVERT: C 409 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6341 (p0) outliers start: 26 outliers final: 19 residues processed: 152 average time/residue: 1.5176 time to fit residues: 256.2733 Evaluate side-chains 153 residues out of total 1897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 409 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 474 TYR Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.0040 chunk 174 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 179 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050147 restraints weight = 104578.567| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.04 r_work: 0.2801 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18806 Z= 0.185 Angle : 0.620 13.242 25551 Z= 0.285 Chirality : 0.039 0.211 2841 Planarity : 0.003 0.051 3114 Dihedral : 11.066 137.523 3023 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.14 % Rotamer: Outliers : 1.36 % Allowed : 15.42 % Favored : 83.22 % 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: 1.71 (0.17), residues: 970 sheet: -0.31 (0.34), residues: 227 loop : -0.46 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 182 HIS 0.004 0.001 HIS C 366 PHE 0.011 0.001 PHE B 344 TYR 0.012 0.001 TYR B 554 ARG 0.007 0.000 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6190.64 seconds wall clock time: 112 minutes 30.40 seconds (6750.40 seconds total)