Starting phenix.real_space_refine on Thu May 9 20:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugs_42234/05_2024/8ugs_42234_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8909 2.51 5 N 2351 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ASP 584": "OD1" <-> "OD2" Residue "B TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 13961 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6682 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain: "B" Number of atoms: 6634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6634 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 32, 'TRANS': 783} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 269 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain breaks: 1 Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 280 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.75, per 1000 atoms: 0.56 Number of scatterers: 13961 At special positions: 0 Unit cell: (95.63, 125.76, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 4 15.00 Mg 2 11.99 O 2596 8.00 N 2351 7.00 C 8909 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=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 53.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.661A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 205 through 249 removed outlier: 4.144A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.541A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 414 through 458 removed outlier: 3.822A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 464 through 467 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.607A pdb=" N ILE A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.555A pdb=" N PHE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 535' Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 561 through 577 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 626 through 640 Processing helix chain 'A' and resid 652 through 668 Processing helix chain 'A' and resid 671 through 690 removed outlier: 5.165A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 728 through 752 removed outlier: 4.095A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.674A pdb=" N LEU A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'A' and resid 793 through 820 Proline residue: A 797 - end of helix removed outlier: 3.604A pdb=" N ILE A 802 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 803 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 67 Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.738A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 203 through 248 removed outlier: 3.719A pdb=" N ASN B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 5.304A pdb=" N ALA B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 412 through 456 removed outlier: 3.513A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 513 through 526 Processing helix chain 'B' and resid 529 through 532 No H-bonds generated for 'chain 'B' and resid 529 through 532' Processing helix chain 'B' and resid 537 through 550 Processing helix chain 'B' and resid 560 through 574 removed outlier: 6.258A pdb=" N VAL B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 581 removed outlier: 3.523A pdb=" N TYR B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 581' Processing helix chain 'B' and resid 584 through 595 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.548A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 688 removed outlier: 3.574A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 703 through 718 Processing helix chain 'B' and resid 720 through 723 No H-bonds generated for 'chain 'B' and resid 720 through 723' Processing helix chain 'B' and resid 726 through 749 removed outlier: 4.562A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 Proline residue: B 768 - end of helix Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 791 through 821 removed outlier: 3.512A pdb=" N LEU B 794 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Proline residue: B 795 - end of helix removed outlier: 3.660A pdb=" N ASP B 798 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 799 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing sheet with id= A, first strand: chain 'A' and resid 106 through 112 removed outlier: 6.721A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.236A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 184 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 360 removed outlier: 4.077A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 110 removed outlier: 6.810A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 14.321A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 328 through 331 removed outlier: 7.051A pdb=" N LEU B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 316 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 318 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 273 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2370 1.31 - 1.44: 3734 1.44 - 1.57: 7991 1.57 - 1.69: 12 1.69 - 1.82: 174 Bond restraints: 14281 Sorted by residual: bond pdb=" C6 PCG A 901 " pdb=" O6 PCG A 901 " ideal model delta sigma weight residual 1.220 1.184 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C6 PCG B 904 " pdb=" O6 PCG B 904 " ideal model delta sigma weight residual 1.220 1.184 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C6 PCG B 901 " pdb=" O6 PCG B 901 " ideal model delta sigma weight residual 1.220 1.184 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C6 PCG A 904 " pdb=" O6 PCG A 904 " ideal model delta sigma weight residual 1.220 1.185 0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" O1A PCG B 901 " pdb=" PA PCG B 901 " ideal model delta sigma weight residual 1.681 1.647 0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 14276 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.75: 297 105.75 - 112.82: 7526 112.82 - 119.89: 4721 119.89 - 126.95: 6603 126.95 - 134.02: 173 Bond angle restraints: 19320 Sorted by residual: angle pdb=" C ARG A 40 " pdb=" CA ARG A 40 " pdb=" CB ARG A 40 " ideal model delta sigma weight residual 115.79 109.81 5.98 1.19e+00 7.06e-01 2.53e+01 angle pdb=" CB MET B 155 " pdb=" CG MET B 155 " pdb=" SD MET B 155 " ideal model delta sigma weight residual 112.70 125.35 -12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CA GLN A 285 " pdb=" CB GLN A 285 " pdb=" CG GLN A 285 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB LYS A 186 " pdb=" CG LYS A 186 " pdb=" CD LYS A 186 " ideal model delta sigma weight residual 111.30 118.84 -7.54 2.30e+00 1.89e-01 1.08e+01 angle pdb=" N LYS A 186 " pdb=" CA LYS A 186 " pdb=" C LYS A 186 " ideal model delta sigma weight residual 113.43 109.43 4.00 1.26e+00 6.30e-01 1.01e+01 ... (remaining 19315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.12: 7465 20.12 - 40.24: 915 40.24 - 60.36: 192 60.36 - 80.48: 34 80.48 - 100.60: 12 Dihedral angle restraints: 8618 sinusoidal: 3614 harmonic: 5004 Sorted by residual: dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N ASN B 403 " pdb=" CA ASN B 403 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO B 41 " pdb=" C PRO B 41 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " ideal model delta harmonic sigma weight residual 180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" C4' PCG B 904 " pdb=" C5' PCG B 904 " pdb=" O5' PCG B 904 " pdb=" PA PCG B 904 " ideal model delta sinusoidal sigma weight residual 53.20 -47.40 100.60 1 3.00e+01 1.11e-03 1.26e+01 ... (remaining 8615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1609 0.040 - 0.081: 374 0.081 - 0.121: 119 0.121 - 0.161: 1 0.161 - 0.201: 1 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CB VAL B 154 " pdb=" CA VAL B 154 " pdb=" CG1 VAL B 154 " pdb=" CG2 VAL B 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A 537 " pdb=" N ILE A 537 " pdb=" C ILE A 537 " pdb=" CB ILE A 537 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 311 " pdb=" N ILE B 311 " pdb=" C ILE B 311 " pdb=" CB ILE B 311 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 2101 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 132 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 133 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 597 " 0.017 2.00e-02 2.50e+03 1.66e-02 4.13e+00 pdb=" CG HIS B 597 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS B 597 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 597 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 597 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 597 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 19 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 20 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " 0.024 5.00e-02 4.00e+02 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 140 2.60 - 3.18: 12210 3.18 - 3.75: 22529 3.75 - 4.33: 30375 4.33 - 4.90: 51025 Nonbonded interactions: 116279 Sorted by model distance: nonbonded pdb="MG MG B 903 " pdb=" O1A PCG B 904 " model vdw 2.028 2.170 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.075 2.230 nonbonded pdb="MG MG A 903 " pdb=" O1A PCG A 904 " model vdw 2.088 2.170 nonbonded pdb=" CG HIS B 597 " pdb="ZN ZN B 902 " model vdw 2.198 1.960 nonbonded pdb=" OD1 ASN A 607 " pdb=" NE2 GLN A 745 " model vdw 2.257 2.520 ... (remaining 116274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 12 through 86) } 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: 0.820 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: 4.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 40.500 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.038 14281 Z= 0.170 Angle : 0.532 12.652 19320 Z= 0.282 Chirality : 0.037 0.201 2104 Planarity : 0.003 0.051 2482 Dihedral : 17.878 100.598 5372 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 18.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.21), residues: 1689 helix: 1.72 (0.17), residues: 954 sheet: 0.68 (0.44), residues: 139 loop : -0.16 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.017 0.001 HIS B 597 PHE 0.018 0.001 PHE B 163 TYR 0.011 0.001 TYR B 273 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8012 (pttp) cc_final: 0.7803 (mtmm) REVERT: A 193 MET cc_start: 0.8306 (ptm) cc_final: 0.7805 (ppp) REVERT: A 222 MET cc_start: 0.8470 (mmm) cc_final: 0.7910 (mmt) REVERT: A 286 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8514 (mtpp) REVERT: A 296 MET cc_start: 0.7913 (mmm) cc_final: 0.7473 (mmm) REVERT: A 652 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6936 (tmm160) REVERT: A 756 ASN cc_start: 0.8657 (t0) cc_final: 0.8412 (t0) REVERT: A 761 MET cc_start: 0.8545 (mtt) cc_final: 0.8309 (mtm) REVERT: B 96 MET cc_start: 0.8842 (mmm) cc_final: 0.8611 (mmm) REVERT: B 141 HIS cc_start: 0.8119 (t-170) cc_final: 0.7862 (t-170) REVERT: B 190 ILE cc_start: 0.8738 (mt) cc_final: 0.8530 (mp) REVERT: B 209 PHE cc_start: 0.8474 (t80) cc_final: 0.8273 (t80) REVERT: B 681 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8563 (mtpt) REVERT: B 808 LYS cc_start: 0.9008 (tptm) cc_final: 0.8233 (tptm) outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.3037 time to fit residues: 82.3504 Evaluate side-chains 141 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0270 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS C 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14281 Z= 0.167 Angle : 0.503 6.098 19320 Z= 0.265 Chirality : 0.039 0.171 2104 Planarity : 0.004 0.050 2482 Dihedral : 4.777 88.603 1878 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 2.10 % Allowed : 17.90 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.21), residues: 1689 helix: 1.57 (0.17), residues: 965 sheet: 0.59 (0.42), residues: 140 loop : -0.05 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 559 HIS 0.006 0.001 HIS B 658 PHE 0.020 0.001 PHE B 209 TYR 0.026 0.001 TYR A 49 ARG 0.002 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8334 (ptm) cc_final: 0.6708 (ppp) REVERT: A 286 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8404 (mtpp) REVERT: A 296 MET cc_start: 0.7633 (mmm) cc_final: 0.7388 (mmm) REVERT: A 700 TYR cc_start: 0.6911 (t80) cc_final: 0.6623 (t80) REVERT: A 756 ASN cc_start: 0.8672 (t0) cc_final: 0.8411 (t0) REVERT: A 761 MET cc_start: 0.8502 (mtt) cc_final: 0.8271 (mtp) REVERT: B 174 ASN cc_start: 0.6878 (OUTLIER) cc_final: 0.6055 (p0) REVERT: B 209 PHE cc_start: 0.8427 (t80) cc_final: 0.8044 (t80) REVERT: B 671 LEU cc_start: 0.8068 (tt) cc_final: 0.7823 (mt) REVERT: B 681 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8552 (mtpp) REVERT: B 714 MET cc_start: 0.9235 (mmm) cc_final: 0.9006 (mmm) REVERT: B 766 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7315 (mp0) REVERT: D 17 MET cc_start: 0.6721 (mmm) cc_final: 0.6509 (mmm) outliers start: 32 outliers final: 14 residues processed: 170 average time/residue: 0.3049 time to fit residues: 74.1483 Evaluate side-chains 140 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14281 Z= 0.187 Angle : 0.497 7.228 19320 Z= 0.256 Chirality : 0.038 0.142 2104 Planarity : 0.004 0.050 2482 Dihedral : 4.722 84.973 1878 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 2.23 % Allowed : 17.44 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.21), residues: 1689 helix: 1.49 (0.17), residues: 961 sheet: 0.27 (0.41), residues: 142 loop : -0.10 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.008 0.001 HIS B 141 PHE 0.014 0.001 PHE B 209 TYR 0.012 0.001 TYR B 97 ARG 0.003 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7844 (m) REVERT: A 176 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6099 (m-40) REVERT: A 193 MET cc_start: 0.8329 (ptm) cc_final: 0.6692 (ppp) REVERT: A 286 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8442 (mtpp) REVERT: A 638 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8999 (mt) REVERT: A 756 ASN cc_start: 0.8675 (t0) cc_final: 0.8438 (t0) REVERT: B 174 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6076 (p0) REVERT: B 209 PHE cc_start: 0.8410 (t80) cc_final: 0.7886 (t80) REVERT: B 681 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8349 (mtpp) REVERT: B 712 MET cc_start: 0.8365 (mpp) cc_final: 0.7892 (mpp) REVERT: B 714 MET cc_start: 0.9267 (mmm) cc_final: 0.8729 (mmm) outliers start: 34 outliers final: 21 residues processed: 159 average time/residue: 0.2776 time to fit residues: 65.9014 Evaluate side-chains 147 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14281 Z= 0.196 Angle : 0.497 7.260 19320 Z= 0.256 Chirality : 0.038 0.149 2104 Planarity : 0.004 0.051 2482 Dihedral : 4.638 78.958 1878 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 2.56 % Allowed : 17.57 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.21), residues: 1689 helix: 1.49 (0.17), residues: 960 sheet: 0.34 (0.42), residues: 140 loop : -0.13 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.006 0.001 HIS B 141 PHE 0.013 0.001 PHE B 563 TYR 0.012 0.001 TYR B 97 ARG 0.005 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8472 (mtp-110) cc_final: 0.8051 (ptm160) REVERT: A 86 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7953 (m) REVERT: A 176 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.6188 (m-40) REVERT: A 193 MET cc_start: 0.8378 (ptm) cc_final: 0.7982 (ppp) REVERT: A 286 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8430 (mtpp) REVERT: A 571 MET cc_start: 0.9010 (tpp) cc_final: 0.8799 (tpp) REVERT: A 638 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8949 (mt) REVERT: B 174 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.6251 (p0) REVERT: B 209 PHE cc_start: 0.8388 (t80) cc_final: 0.7901 (t80) REVERT: B 681 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8335 (mtpp) REVERT: B 712 MET cc_start: 0.8535 (mpp) cc_final: 0.8197 (mmm) outliers start: 39 outliers final: 18 residues processed: 157 average time/residue: 0.2694 time to fit residues: 63.0695 Evaluate side-chains 139 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14281 Z= 0.185 Angle : 0.482 8.490 19320 Z= 0.248 Chirality : 0.038 0.129 2104 Planarity : 0.004 0.051 2482 Dihedral : 4.226 54.304 1878 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 2.82 % Allowed : 17.64 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.21), residues: 1689 helix: 1.54 (0.17), residues: 959 sheet: 0.21 (0.42), residues: 142 loop : -0.12 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.004 0.001 HIS B 658 PHE 0.013 0.001 PHE B 588 TYR 0.012 0.001 TYR B 97 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8041 (ptm160) REVERT: A 86 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7997 (m) REVERT: A 176 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6131 (m-40) REVERT: A 193 MET cc_start: 0.8325 (ptm) cc_final: 0.7923 (ppp) REVERT: A 286 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8400 (mtpp) REVERT: A 579 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: A 638 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8947 (mt) REVERT: B 174 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6283 (p0) REVERT: B 293 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (tt) REVERT: B 681 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8332 (mtpp) outliers start: 43 outliers final: 24 residues processed: 160 average time/residue: 0.2743 time to fit residues: 65.1127 Evaluate side-chains 151 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 0.0070 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14281 Z= 0.160 Angle : 0.472 8.570 19320 Z= 0.244 Chirality : 0.037 0.133 2104 Planarity : 0.004 0.050 2482 Dihedral : 3.774 26.106 1878 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 2.49 % Allowed : 18.23 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.21), residues: 1689 helix: 1.60 (0.18), residues: 959 sheet: 0.24 (0.42), residues: 142 loop : -0.15 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.004 0.001 HIS B 658 PHE 0.013 0.001 PHE B 209 TYR 0.011 0.001 TYR A 275 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.8094 (ptm160) REVERT: A 86 CYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7783 (m) REVERT: A 193 MET cc_start: 0.8429 (ptm) cc_final: 0.6763 (ppp) REVERT: A 579 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8599 (mttm) REVERT: A 638 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8943 (mt) REVERT: B 174 ASN cc_start: 0.7056 (OUTLIER) cc_final: 0.6435 (p0) REVERT: B 681 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8327 (mtpp) outliers start: 38 outliers final: 24 residues processed: 156 average time/residue: 0.2722 time to fit residues: 63.4589 Evaluate side-chains 148 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14281 Z= 0.274 Angle : 0.546 9.192 19320 Z= 0.281 Chirality : 0.040 0.143 2104 Planarity : 0.004 0.053 2482 Dihedral : 3.932 22.829 1878 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.56 % Allowed : 18.82 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.21), residues: 1689 helix: 1.46 (0.17), residues: 960 sheet: 0.20 (0.42), residues: 145 loop : -0.16 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 697 HIS 0.006 0.001 HIS A 630 PHE 0.015 0.001 PHE B 588 TYR 0.015 0.002 TYR B 97 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8124 (ptm160) REVERT: A 176 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.6156 (m-40) REVERT: A 193 MET cc_start: 0.8422 (ptm) cc_final: 0.7901 (ppp) REVERT: A 579 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (mttm) REVERT: A 638 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8987 (mt) REVERT: B 26 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7867 (tmtt) REVERT: B 155 MET cc_start: 0.9154 (mmp) cc_final: 0.8926 (mmm) REVERT: B 174 ASN cc_start: 0.7012 (OUTLIER) cc_final: 0.6361 (p0) REVERT: B 293 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 437 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8568 (ttpt) REVERT: B 681 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8338 (mtpp) REVERT: C 83 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6629 (tp-100) outliers start: 39 outliers final: 29 residues processed: 154 average time/residue: 0.2743 time to fit residues: 63.4309 Evaluate side-chains 155 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14281 Z= 0.164 Angle : 0.495 10.017 19320 Z= 0.253 Chirality : 0.038 0.142 2104 Planarity : 0.004 0.051 2482 Dihedral : 3.797 21.381 1878 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.43 % Allowed : 19.15 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.21), residues: 1689 helix: 1.57 (0.17), residues: 958 sheet: 0.20 (0.43), residues: 142 loop : -0.19 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.004 0.001 HIS B 658 PHE 0.012 0.001 PHE C 30 TYR 0.011 0.001 TYR A 275 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6260 (m-40) REVERT: A 193 MET cc_start: 0.8397 (ptm) cc_final: 0.6551 (ppp) REVERT: A 579 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8655 (mttm) REVERT: A 638 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8876 (mt) REVERT: B 155 MET cc_start: 0.9143 (mmp) cc_final: 0.8910 (mmm) REVERT: B 174 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6399 (p0) REVERT: B 293 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 681 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8319 (mtpp) REVERT: C 83 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6605 (tp-100) outliers start: 37 outliers final: 27 residues processed: 155 average time/residue: 0.2692 time to fit residues: 62.4362 Evaluate side-chains 154 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.0570 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14281 Z= 0.177 Angle : 0.504 10.127 19320 Z= 0.256 Chirality : 0.038 0.143 2104 Planarity : 0.004 0.052 2482 Dihedral : 3.749 21.983 1878 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 2.30 % Allowed : 19.21 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1689 helix: 1.57 (0.18), residues: 958 sheet: 0.19 (0.43), residues: 142 loop : -0.20 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 697 HIS 0.004 0.001 HIS B 658 PHE 0.012 0.001 PHE B 563 TYR 0.013 0.001 TYR B 783 ARG 0.002 0.000 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8247 (mtp) cc_final: 0.8002 (mtp) REVERT: A 176 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6248 (m-40) REVERT: A 193 MET cc_start: 0.8445 (ptm) cc_final: 0.6571 (ppp) REVERT: A 579 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8670 (mttm) REVERT: A 638 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8944 (mt) REVERT: A 712 MET cc_start: 0.8837 (ttp) cc_final: 0.8609 (ttp) REVERT: B 174 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6414 (p0) REVERT: B 293 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 681 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8323 (mtpp) REVERT: C 83 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6626 (tp-100) outliers start: 35 outliers final: 26 residues processed: 152 average time/residue: 0.2851 time to fit residues: 64.2214 Evaluate side-chains 152 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 0.3980 chunk 110 optimal weight: 0.0370 chunk 167 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14281 Z= 0.152 Angle : 0.503 10.663 19320 Z= 0.253 Chirality : 0.037 0.135 2104 Planarity : 0.004 0.050 2482 Dihedral : 3.673 20.856 1878 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 2.03 % Allowed : 19.61 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.21), residues: 1689 helix: 1.59 (0.18), residues: 955 sheet: 0.19 (0.44), residues: 142 loop : -0.16 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 PHE 0.011 0.001 PHE B 209 TYR 0.013 0.001 TYR B 783 ARG 0.001 0.000 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.8236 (ptm160) REVERT: A 82 MET cc_start: 0.8105 (mtp) cc_final: 0.7828 (mtp) REVERT: A 176 ASN cc_start: 0.6363 (OUTLIER) cc_final: 0.6085 (m-40) REVERT: A 193 MET cc_start: 0.8328 (ptm) cc_final: 0.6612 (ppp) REVERT: A 579 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8646 (mttm) REVERT: A 638 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8952 (mt) REVERT: B 9 HIS cc_start: 0.8268 (t-170) cc_final: 0.7886 (t70) REVERT: B 174 ASN cc_start: 0.7028 (OUTLIER) cc_final: 0.6479 (p0) REVERT: B 209 PHE cc_start: 0.8296 (t80) cc_final: 0.8071 (t80) REVERT: B 293 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7949 (tt) REVERT: B 569 MET cc_start: 0.9006 (tpt) cc_final: 0.8800 (tpp) REVERT: B 681 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8329 (mtpp) REVERT: C 83 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6594 (tp-100) outliers start: 31 outliers final: 25 residues processed: 150 average time/residue: 0.2617 time to fit residues: 59.0890 Evaluate side-chains 153 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 579 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 367 ASN Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 0.0010 chunk 133 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** 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 = 0.3733 r_free = 0.3733 target = 0.096701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075678 restraints weight = 35753.629| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.83 r_work: 0.3205 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14281 Z= 0.180 Angle : 0.512 10.447 19320 Z= 0.258 Chirality : 0.038 0.142 2104 Planarity : 0.004 0.051 2482 Dihedral : 3.666 21.649 1878 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 2.16 % Allowed : 20.07 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.21), residues: 1689 helix: 1.59 (0.18), residues: 955 sheet: 0.18 (0.43), residues: 142 loop : -0.14 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 561 HIS 0.003 0.001 HIS B 658 PHE 0.013 0.001 PHE B 588 TYR 0.012 0.001 TYR B 783 ARG 0.002 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.69 seconds wall clock time: 54 minutes 3.22 seconds (3243.22 seconds total)