Starting phenix.real_space_refine on Sat Feb 17 09:46:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qcs_4511/02_2024/6qcs_4511_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.026 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 36 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11446 2.51 5 N 3147 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 438": "NH1" <-> "NH2" Residue "C PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18278 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5740 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 26, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5881 Classifications: {'peptide': 750} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Chain: "C" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5901 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 713} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 139 Unusual residues: {'GTG': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 1, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.10, per 1000 atoms: 0.55 Number of scatterers: 18278 At special positions: 0 Unit cell: (126.327, 127.158, 123.834, 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 132 16.00 P 36 15.00 Mg 2 11.99 O 3515 8.00 N 3147 7.00 C 11446 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: 6.91 Conformation dependent library (CDL) restraints added in 3.2 seconds 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 21 sheets defined 40.1% alpha, 11.1% beta 6 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 8.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.653A pdb=" N HIS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 165 through 183 removed outlier: 3.678A pdb=" N LEU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' 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 347 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 430 through 448 removed outlier: 3.755A pdb=" N TYR A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.202A pdb=" N GLN A 579 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN A 582 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 586 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 593 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 629 through 645 removed outlier: 3.729A pdb=" N TYR A 644 " --> pdb=" O CYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 669 removed outlier: 4.380A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.542A pdb=" N GLU A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.672A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 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 removed outlier: 3.634A pdb=" N THR B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 removed outlier: 3.668A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.705A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.607A 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 249 through 265 removed outlier: 3.767A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 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 removed outlier: 3.686A pdb=" N ALA B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 340 through 344 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 removed outlier: 3.614A pdb=" N LYS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 416 through 425 Processing helix chain 'B' and resid 455 through 472 removed outlier: 3.593A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 518 through 534 removed outlier: 3.855A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.835A 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 572 through 581 removed outlier: 3.857A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (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 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' 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 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 617 through 623 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 671 through 674 Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.646A pdb=" N TYR B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 690 " --> pdb=" O GLN B 686 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.665A pdb=" N MET B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 748 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 183 No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.400A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 274 removed outlier: 5.006A pdb=" N VAL C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.939A 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 309 through 317 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 449 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 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 543 through 556 Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 579 through 584 removed outlier: 4.582A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 606 Processing helix chain 'C' and resid 612 through 622 Proline residue: C 620 - end of helix 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 719 removed outlier: 3.637A pdb=" N LYS C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) 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 removed outlier: 6.078A pdb=" N GLU A 144 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY A 122 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N MET A 146 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 537 through 545 removed outlier: 6.686A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 614 through 620 removed outlier: 6.821A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 619 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS A 623 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 179 through 187 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= I, first strand: chain 'B' and resid 482 through 485 removed outlier: 3.823A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 488 through 491 Processing sheet with id= M, first strand: chain 'B' and resid 641 through 644 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 324 through 327 removed outlier: 5.086A pdb=" N ARG C 373 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER C 379 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 482 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 340 through 347 Processing sheet with id= R, first strand: chain 'C' and resid 639 through 641 Processing sheet with id= S, first strand: chain 'C' and resid 659 through 662 Processing sheet with id= T, first strand: chain 'C' and resid 724 through 729 removed outlier: 3.852A pdb=" N GLU C 724 " --> pdb=" O LYS C 740 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 80 through 84 removed outlier: 3.983A pdb=" N MET C 92 " --> pdb=" O THR C 81 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 7.35 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: 4429 1.33 - 1.45: 3707 1.45 - 1.57: 10266 1.57 - 1.69: 69 1.69 - 1.81: 224 Bond restraints: 18695 Sorted by residual: bond pdb=" C2E GTG M 1 " pdb=" C3E GTG M 1 " ideal model delta sigma weight residual 1.254 1.494 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C3D GTG M 1 " pdb=" C4D GTG M 1 " ideal model delta sigma weight residual 1.298 1.528 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.538 1.325 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C5A GTG M 1 " pdb=" C6A GTG M 1 " ideal model delta sigma weight residual 1.539 1.338 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C4B GTG M 1 " pdb=" N3B GTG M 1 " ideal model delta sigma weight residual 1.499 1.340 0.159 2.00e-02 2.50e+03 6.31e+01 ... (remaining 18690 not shown) Histogram of bond angle deviations from ideal: 95.06 - 102.91: 212 102.91 - 110.76: 6127 110.76 - 118.61: 8732 118.61 - 126.46: 9946 126.46 - 134.31: 341 Bond angle restraints: 25358 Sorted by residual: angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C4A GTG M 1 " ideal model delta sigma weight residual 93.21 123.41 -30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C8A GTG M 1 " ideal model delta sigma weight residual 157.61 128.15 29.46 3.00e+00 1.11e-01 9.65e+01 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C4B GTG M 1 " ideal model delta sigma weight residual 152.69 125.08 27.61 3.00e+00 1.11e-01 8.47e+01 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C8B GTG M 1 " ideal model delta sigma weight residual 99.21 126.53 -27.32 3.00e+00 1.11e-01 8.30e+01 angle pdb=" C VAL A 720 " pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 121.54 131.95 -10.41 1.91e+00 2.74e-01 2.97e+01 ... (remaining 25353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10271 17.90 - 35.80: 847 35.80 - 53.69: 230 53.69 - 71.59: 64 71.59 - 89.49: 30 Dihedral angle restraints: 11442 sinusoidal: 5063 harmonic: 6379 Sorted by residual: dihedral pdb=" CA GLY B 125 " pdb=" C GLY B 125 " pdb=" N ARG B 126 " pdb=" CA ARG B 126 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA SER B 442 " pdb=" C SER B 442 " pdb=" N SER B 443 " pdb=" CA SER B 443 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual 254.00 179.51 74.49 1 1.70e+01 3.46e-03 2.43e+01 ... (remaining 11439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2585 0.082 - 0.165: 222 0.165 - 0.247: 6 0.247 - 0.329: 2 0.329 - 0.411: 1 Chirality restraints: 2816 Sorted by residual: chirality pdb=" C3D GTG M 1 " pdb=" C2D GTG M 1 " pdb=" C4D GTG M 1 " pdb=" O3D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3E GTG M 1 " pdb=" C2E GTG M 1 " pdb=" C4E GTG M 1 " pdb=" O3E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.43 -2.75 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1' A M 3 " pdb=" O4' A M 3 " pdb=" C2' A M 3 " pdb=" N9 A M 3 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2813 not shown) Planarity restraints: 3130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 656 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO C 657 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 657 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 657 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 370 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO B 371 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO A 217 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.031 5.00e-02 4.00e+02 ... (remaining 3127 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 551 2.69 - 3.24: 16059 3.24 - 3.80: 28754 3.80 - 4.35: 39539 4.35 - 4.90: 64856 Nonbonded interactions: 149759 Sorted by model distance: nonbonded pdb=" OE1 GLU A 81 " pdb="MG MG A 801 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.160 2.170 nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR B 226 " pdb=" O ARG B 350 " model vdw 2.267 2.440 nonbonded pdb=" O LYS A 16 " pdb=" OG1 THR A 20 " model vdw 2.304 2.440 ... (remaining 149754 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=1.00 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: 2.180 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: 0.010 Extract box with map and model: 7.040 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 52.760 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.240 18695 Z= 0.516 Angle : 0.853 30.202 25358 Z= 0.439 Chirality : 0.049 0.411 2816 Planarity : 0.006 0.065 3130 Dihedral : 15.337 89.491 7332 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 5.64 % Allowed : 7.99 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -3.72 (0.14), residues: 2199 helix: -2.45 (0.12), residues: 938 sheet: -1.68 (0.30), residues: 265 loop : -2.63 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 437 HIS 0.005 0.001 HIS B 711 PHE 0.020 0.002 PHE C 698 TYR 0.023 0.002 TYR A 644 ARG 0.004 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 243 time to evaluate : 2.006 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: C 218 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7711 (mpt-90) REVERT: C 534 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8224 (m) REVERT: C 555 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7978 (tt) REVERT: C 654 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8124 (pttt) REVERT: C 686 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: C 705 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7358 (t0) outliers start: 108 outliers final: 27 residues processed: 337 average time/residue: 0.3485 time to fit residues: 171.8995 Evaluate side-chains 182 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.0060 chunk 168 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 152 GLN A 222 ASN A 319 GLN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 666 GLN A 693 ASN B 47 HIS B 104 GLN B 108 GLN B 137 GLN B 247 GLN B 292 ASN B 310 ASN B 670 ASN B 680 ASN B 710 GLN C 11 GLN C 247 HIS C 437 GLN C 466 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18695 Z= 0.158 Angle : 0.501 8.846 25358 Z= 0.261 Chirality : 0.039 0.218 2816 Planarity : 0.004 0.043 3130 Dihedral : 11.654 87.705 2950 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.24 % Allowed : 12.47 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -2.04 (0.16), residues: 2199 helix: -0.56 (0.16), residues: 946 sheet: -1.46 (0.29), residues: 279 loop : -2.07 (0.17), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS C 366 PHE 0.010 0.001 PHE B 449 TYR 0.011 0.001 TYR A 106 ARG 0.005 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.026 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: 0.7508 (mmm) cc_final: 0.7160 (mmm) REVERT: A 53 PHE cc_start: 0.6803 (m-10) cc_final: 0.6505 (m-10) REVERT: A 141 ASN cc_start: 0.7444 (t0) cc_final: 0.7168 (t0) REVERT: B 104 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7095 (tm130) REVERT: C 218 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7981 (mpt-90) REVERT: C 412 MET cc_start: 0.7548 (tmm) cc_final: 0.7329 (tmm) REVERT: C 449 ASP cc_start: 0.7931 (m-30) cc_final: 0.7688 (m-30) REVERT: C 555 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7961 (tt) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.3273 time to fit residues: 92.8104 Evaluate side-chains 158 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS C 466 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18695 Z= 0.291 Angle : 0.526 7.097 25358 Z= 0.272 Chirality : 0.041 0.209 2816 Planarity : 0.004 0.036 3130 Dihedral : 11.363 82.450 2926 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.51 % Allowed : 13.20 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -1.22 (0.17), residues: 2199 helix: 0.25 (0.17), residues: 944 sheet: -1.19 (0.30), residues: 270 loop : -1.72 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 437 HIS 0.003 0.001 HIS B 711 PHE 0.013 0.001 PHE C 448 TYR 0.016 0.001 TYR C 246 ARG 0.004 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6507 (tmm) cc_final: 0.5891 (ttt) REVERT: A 53 PHE cc_start: 0.6915 (m-10) cc_final: 0.6611 (m-10) REVERT: A 133 TRP cc_start: 0.7994 (m100) cc_final: 0.7666 (m100) REVERT: B 104 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7387 (tm130) REVERT: C 218 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6371 (mpt-90) REVERT: C 412 MET cc_start: 0.7879 (tmm) cc_final: 0.7666 (tmm) REVERT: C 449 ASP cc_start: 0.8009 (m-30) cc_final: 0.7785 (m-30) REVERT: C 465 ILE cc_start: 0.2960 (OUTLIER) cc_final: 0.2750 (pp) REVERT: C 469 MET cc_start: 0.5602 (mtt) cc_final: 0.5286 (mtp) REVERT: C 529 MET cc_start: 0.8015 (tpp) cc_final: 0.7730 (ttt) REVERT: C 555 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 48 outliers final: 30 residues processed: 179 average time/residue: 0.3172 time to fit residues: 86.6990 Evaluate side-chains 167 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18695 Z= 0.172 Angle : 0.466 8.141 25358 Z= 0.239 Chirality : 0.039 0.206 2816 Planarity : 0.003 0.033 3130 Dihedral : 11.142 80.242 2921 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.09 % Allowed : 14.35 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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 (0.17), residues: 2199 helix: 0.80 (0.17), residues: 939 sheet: -1.01 (0.30), residues: 270 loop : -1.48 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.006 0.001 HIS C 463 PHE 0.009 0.001 PHE A 629 TYR 0.010 0.001 TYR B 554 ARG 0.005 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 139 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: A 51 MET cc_start: 0.7928 (mmm) cc_final: 0.7719 (mmm) REVERT: A 133 TRP cc_start: 0.7948 (m100) cc_final: 0.7515 (m100) REVERT: A 141 ASN cc_start: 0.7361 (t0) cc_final: 0.6928 (t0) REVERT: A 143 MET cc_start: 0.8022 (ttt) cc_final: 0.7750 (ttt) REVERT: A 571 MET cc_start: 0.8131 (mtp) cc_final: 0.7893 (mtp) REVERT: B 104 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7358 (tm130) REVERT: C 292 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7301 (t0) REVERT: C 412 MET cc_start: 0.7815 (tmm) cc_final: 0.7517 (tmm) REVERT: C 529 MET cc_start: 0.8013 (tpp) cc_final: 0.7754 (ttt) REVERT: C 555 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8048 (tt) outliers start: 40 outliers final: 23 residues processed: 174 average time/residue: 0.3126 time to fit residues: 84.0125 Evaluate side-chains 154 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 0.4980 chunk 192 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 745 HIS C 466 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 18695 Z= 0.545 Angle : 0.655 9.458 25358 Z= 0.337 Chirality : 0.046 0.191 2816 Planarity : 0.004 0.065 3130 Dihedral : 11.441 87.728 2914 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.61 % Allowed : 14.41 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.97 (0.17), residues: 2199 helix: 0.47 (0.17), residues: 938 sheet: -1.10 (0.31), residues: 254 loop : -1.58 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 437 HIS 0.005 0.001 HIS C 463 PHE 0.020 0.002 PHE A 132 TYR 0.023 0.002 TYR C 246 ARG 0.012 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5986 (ttt) cc_final: 0.5719 (ttt) REVERT: A 43 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: A 133 TRP cc_start: 0.8173 (m100) cc_final: 0.7910 (m100) REVERT: A 141 ASN cc_start: 0.7522 (t0) cc_final: 0.7109 (t0) REVERT: A 143 MET cc_start: 0.8041 (ttt) cc_final: 0.7761 (ttt) REVERT: B 104 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7564 (tm130) REVERT: C 72 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8712 (tm) REVERT: C 218 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6557 (mpt-90) REVERT: C 412 MET cc_start: 0.7879 (tmm) cc_final: 0.7189 (tmm) REVERT: C 555 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8234 (tt) outliers start: 50 outliers final: 35 residues processed: 176 average time/residue: 0.3131 time to fit residues: 85.7106 Evaluate side-chains 163 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 HIS Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18695 Z= 0.134 Angle : 0.471 7.763 25358 Z= 0.242 Chirality : 0.038 0.191 2816 Planarity : 0.003 0.033 3130 Dihedral : 11.077 83.506 2913 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.04 % Allowed : 15.14 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.38 (0.18), residues: 2199 helix: 1.06 (0.17), residues: 940 sheet: -0.91 (0.31), residues: 264 loop : -1.36 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.002 0.001 HIS C 366 PHE 0.011 0.001 PHE A 223 TYR 0.010 0.001 TYR B 554 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8039 (m100) cc_final: 0.7559 (m100) REVERT: A 141 ASN cc_start: 0.7258 (t0) cc_final: 0.6864 (t0) REVERT: A 143 MET cc_start: 0.7920 (ttt) cc_final: 0.7712 (ttt) REVERT: B 104 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7438 (tm130) REVERT: B 188 LYS cc_start: 0.5811 (tmtt) cc_final: 0.5600 (tptt) REVERT: B 204 ILE cc_start: 0.9197 (tp) cc_final: 0.8985 (tt) REVERT: C 72 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8593 (tm) REVERT: C 218 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.6541 (mpt-90) REVERT: C 412 MET cc_start: 0.7851 (tmm) cc_final: 0.7133 (tmm) REVERT: C 555 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7998 (tt) outliers start: 39 outliers final: 24 residues processed: 166 average time/residue: 0.3243 time to fit residues: 83.3784 Evaluate side-chains 152 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 0.0470 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18695 Z= 0.138 Angle : 0.465 8.923 25358 Z= 0.236 Chirality : 0.038 0.187 2816 Planarity : 0.003 0.035 3130 Dihedral : 10.871 79.325 2911 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.93 % Allowed : 15.14 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.07 (0.18), residues: 2199 helix: 1.34 (0.17), residues: 949 sheet: -0.68 (0.30), residues: 270 loop : -1.26 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 437 HIS 0.002 0.000 HIS A 41 PHE 0.008 0.001 PHE A 223 TYR 0.011 0.001 TYR B 554 ARG 0.005 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8032 (m100) cc_final: 0.7617 (m100) REVERT: A 141 ASN cc_start: 0.7237 (t0) cc_final: 0.6947 (p0) REVERT: B 104 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7468 (tm130) REVERT: B 188 LYS cc_start: 0.5854 (tmtt) cc_final: 0.5552 (tmtt) REVERT: C 72 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8543 (tm) REVERT: C 218 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6556 (mpt-90) REVERT: C 292 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7266 (t70) REVERT: C 555 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8015 (tt) outliers start: 37 outliers final: 21 residues processed: 158 average time/residue: 0.2999 time to fit residues: 74.0961 Evaluate side-chains 150 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18695 Z= 0.216 Angle : 0.491 9.138 25358 Z= 0.248 Chirality : 0.039 0.179 2816 Planarity : 0.003 0.036 3130 Dihedral : 10.903 79.582 2911 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.09 % Allowed : 15.34 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.02 (0.18), residues: 2199 helix: 1.35 (0.17), residues: 950 sheet: -0.59 (0.31), residues: 266 loop : -1.21 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 437 HIS 0.002 0.001 HIS B 711 PHE 0.008 0.001 PHE A 629 TYR 0.011 0.001 TYR B 554 ARG 0.003 0.000 ARG C 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8071 (m100) cc_final: 0.7619 (m100) REVERT: A 143 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: B 104 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7450 (tm130) REVERT: B 188 LYS cc_start: 0.5844 (tmtt) cc_final: 0.5533 (tmtt) REVERT: C 72 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8610 (tm) REVERT: C 218 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6536 (mpt-90) REVERT: C 404 MET cc_start: 0.8160 (mmt) cc_final: 0.7820 (mmt) REVERT: C 555 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8081 (tt) outliers start: 40 outliers final: 30 residues processed: 162 average time/residue: 0.2962 time to fit residues: 76.3140 Evaluate side-chains 161 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 631 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 199 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18695 Z= 0.272 Angle : 0.525 10.787 25358 Z= 0.264 Chirality : 0.040 0.169 2816 Planarity : 0.003 0.038 3130 Dihedral : 10.967 81.592 2911 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 15.34 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: -0.07 (0.18), residues: 2199 helix: 1.27 (0.17), residues: 958 sheet: -0.58 (0.31), residues: 265 loop : -1.23 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.003 0.001 HIS B 711 PHE 0.010 0.001 PHE A 132 TYR 0.013 0.001 TYR C 246 ARG 0.003 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8127 (m100) cc_final: 0.7669 (m100) REVERT: A 143 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7413 (ttt) REVERT: B 104 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7482 (tm130) REVERT: B 188 LYS cc_start: 0.5896 (tmtt) cc_final: 0.5578 (tmtt) REVERT: C 72 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (tm) REVERT: C 218 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.6567 (mpt-90) REVERT: C 233 MET cc_start: 0.8884 (tpp) cc_final: 0.8645 (tpp) REVERT: C 404 MET cc_start: 0.8262 (mmt) cc_final: 0.7888 (mmt) REVERT: C 555 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8105 (tt) REVERT: C 670 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9018 (mt) outliers start: 41 outliers final: 33 residues processed: 159 average time/residue: 0.2911 time to fit residues: 72.9669 Evaluate side-chains 163 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 631 ASN Chi-restraints excluded: chain C residue 670 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.7980 chunk 210 optimal weight: 0.0060 chunk 128 optimal weight: 0.9980 chunk 100 optimal weight: 0.0030 chunk 146 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18695 Z= 0.118 Angle : 0.475 11.901 25358 Z= 0.236 Chirality : 0.038 0.167 2816 Planarity : 0.003 0.041 3130 Dihedral : 10.762 78.170 2911 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.88 % Allowed : 15.92 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.25 (0.18), residues: 2199 helix: 1.58 (0.17), residues: 952 sheet: -0.54 (0.30), residues: 276 loop : -1.05 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.002 0.000 HIS C 366 PHE 0.010 0.001 PHE A 223 TYR 0.015 0.001 TYR B 56 ARG 0.004 0.000 ARG C 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4398 Ramachandran restraints generated. 2199 Oldfield, 0 Emsley, 2199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8053 (m100) cc_final: 0.7499 (m100) REVERT: A 143 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7195 (ttt) REVERT: B 188 LYS cc_start: 0.5804 (tmtt) cc_final: 0.5544 (tmtt) REVERT: C 72 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8521 (tm) REVERT: C 218 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6578 (mpt-90) REVERT: C 404 MET cc_start: 0.8194 (mmt) cc_final: 0.7872 (mmt) REVERT: C 555 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7985 (tt) outliers start: 36 outliers final: 27 residues processed: 161 average time/residue: 0.3024 time to fit residues: 77.1878 Evaluate side-chains 154 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 631 ASN Chi-restraints excluded: chain C residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052924 restraints weight = 50255.824| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.38 r_work: 0.2805 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18695 Z= 0.273 Angle : 0.532 11.843 25358 Z= 0.266 Chirality : 0.041 0.157 2816 Planarity : 0.003 0.051 3130 Dihedral : 10.789 79.446 2906 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.88 % Allowed : 16.02 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.11 % 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: 0.11 (0.18), residues: 2199 helix: 1.43 (0.17), residues: 957 sheet: -0.54 (0.31), residues: 272 loop : -1.13 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 437 HIS 0.003 0.001 HIS B 711 PHE 0.010 0.001 PHE A 132 TYR 0.014 0.001 TYR C 246 ARG 0.002 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.93 seconds wall clock time: 68 minutes 41.75 seconds (4121.75 seconds total)