Starting phenix.real_space_refine on Sun Mar 17 00:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/03_2024/6iro_9720_neut_updated.pdb" } resolution = 3.4 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= 0.006 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 25 5.16 5 C 9253 2.51 5 N 2955 2.21 5 O 3581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 266": "NH1" <-> "NH2" Residue "L ARG 308": "NH1" <-> "NH2" Residue "L ARG 341": "NH1" <-> "NH2" Residue "L ARG 611": "NH1" <-> "NH2" Residue "L ARG 614": "NH1" <-> "NH2" Residue "L ARG 639": "NH1" <-> "NH2" Residue "L ARG 645": "NH1" <-> "NH2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "G PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 83": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16108 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4070 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.41, per 1000 atoms: 0.58 Number of scatterers: 16108 At special positions: 0 Unit cell: (145.52, 131.61, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 294 15.00 O 3581 8.00 N 2955 7.00 C 9253 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: 7.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 3 sheets defined 54.2% alpha, 2.4% beta 126 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'L' and resid 103 through 112 removed outlier: 3.648A pdb=" N LYS L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 123 removed outlier: 3.823A pdb=" N PHE L 122 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 141 removed outlier: 3.600A pdb=" N VAL L 139 " --> pdb=" O GLN L 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 212 Processing helix chain 'L' and resid 227 through 240 removed outlier: 3.661A pdb=" N LEU L 238 " --> pdb=" O PHE L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 267 removed outlier: 5.142A pdb=" N ASN L 258 " --> pdb=" O SER L 255 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 261 " --> pdb=" O ASN L 258 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG L 262 " --> pdb=" O ASN L 259 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE L 264 " --> pdb=" O LEU L 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 265 " --> pdb=" O ARG L 262 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG L 266 " --> pdb=" O GLU L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 288 Processing helix chain 'L' and resid 305 through 308 No H-bonds generated for 'chain 'L' and resid 305 through 308' Processing helix chain 'L' and resid 328 through 330 No H-bonds generated for 'chain 'L' and resid 328 through 330' Processing helix chain 'L' and resid 335 through 342 removed outlier: 3.981A pdb=" N GLU L 342 " --> pdb=" O GLN L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 368 removed outlier: 4.175A pdb=" N TRP L 364 " --> pdb=" O HIS L 361 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN L 368 " --> pdb=" O ALA L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 389 removed outlier: 4.110A pdb=" N TRP L 384 " --> pdb=" O ASP L 380 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE L 385 " --> pdb=" O PHE L 381 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU L 388 " --> pdb=" O TRP L 384 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER L 389 " --> pdb=" O PHE L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 404 No H-bonds generated for 'chain 'L' and resid 401 through 404' Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 435 through 444 removed outlier: 3.587A pdb=" N LYS L 439 " --> pdb=" O SER L 435 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS L 442 " --> pdb=" O LYS L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 477 removed outlier: 3.613A pdb=" N ARG L 473 " --> pdb=" O MET L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 482 Processing helix chain 'L' and resid 496 through 499 No H-bonds generated for 'chain 'L' and resid 496 through 499' Processing helix chain 'L' and resid 502 through 517 removed outlier: 3.581A pdb=" N LYS L 512 " --> pdb=" O ASP L 508 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU L 516 " --> pdb=" O LYS L 512 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU L 517 " --> pdb=" O LYS L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 528 through 540 removed outlier: 3.672A pdb=" N ILE L 533 " --> pdb=" O ARG L 529 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP L 536 " --> pdb=" O ASP L 532 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 555 through 564 removed outlier: 3.710A pdb=" N GLN L 559 " --> pdb=" O GLU L 555 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE L 561 " --> pdb=" O ARG L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 602 through 611 removed outlier: 3.730A pdb=" N ASP L 610 " --> pdb=" O LEU L 606 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG L 611 " --> pdb=" O GLN L 607 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 651 removed outlier: 3.796A pdb=" N GLU L 638 " --> pdb=" O GLU L 634 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 644 " --> pdb=" O ALA L 640 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG L 645 " --> pdb=" O THR L 641 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU L 646 " --> pdb=" O GLN L 642 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP L 647 " --> pdb=" O LYS L 643 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 651 " --> pdb=" O ASP L 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.183A pdb=" N ARG A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.665A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 79 removed outlier: 3.597A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.018A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 removed outlier: 4.092A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 removed outlier: 3.776A pdb=" N ARG E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.739A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 54 through 81 removed outlier: 3.568A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.746A pdb=" N LYS H 105 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 112 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 298 through 301 removed outlier: 6.887A pdb=" N PHE L 248 " --> pdb=" O VAL L 299 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ALA L 301 " --> pdb=" O PHE L 248 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL L 250 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU L 249 " --> pdb=" O TYR L 320 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN L 347 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE L 323 " --> pdb=" O ASN L 347 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU L 349 " --> pdb=" O ILE L 323 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 427 through 431 Processing sheet with id= C, first strand: chain 'L' and resid 592 through 594 removed outlier: 3.536A pdb=" N PHE L 524 " --> pdb=" O VAL L 594 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER L 525 " --> pdb=" O LEU L 576 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 7.41 Time building geometry restraints manager: 8.35 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: 3359 1.33 - 1.45: 5183 1.45 - 1.57: 7825 1.57 - 1.70: 585 1.70 - 1.82: 43 Bond restraints: 16995 Sorted by residual: bond pdb=" C PHE G 25 " pdb=" N PRO G 26 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 7.00e+00 bond pdb=" C3' DG J 66 " pdb=" O3' DG J 66 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.94e+00 bond pdb=" C3' DG I 99 " pdb=" O3' DG I 99 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.82e+00 bond pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" C3' DA I 113 " pdb=" O3' DA I 113 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.42e+00 ... (remaining 16990 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.25: 1175 104.25 - 112.30: 9291 112.30 - 120.36: 7754 120.36 - 128.41: 5625 128.41 - 136.46: 373 Bond angle restraints: 24218 Sorted by residual: angle pdb=" C VAL L 417 " pdb=" N GLU L 418 " pdb=" CA GLU L 418 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.82 129.80 -6.98 1.42e+00 4.96e-01 2.42e+01 angle pdb=" C GLY C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 122.82 129.55 -6.73 1.42e+00 4.96e-01 2.25e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 122.82 129.09 -6.27 1.42e+00 4.96e-01 1.95e+01 ... (remaining 24213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7946 35.64 - 71.29: 1487 71.29 - 106.93: 50 106.93 - 142.58: 4 142.58 - 178.22: 7 Dihedral angle restraints: 9494 sinusoidal: 5809 harmonic: 3685 Sorted by residual: dihedral pdb=" CA LEU A 60 " pdb=" C LEU A 60 " pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta harmonic sigma weight residual -180.00 -143.09 -36.91 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -143.40 -36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA LEU D 99 " pdb=" C LEU D 99 " pdb=" N PRO D 100 " pdb=" CA PRO D 100 " ideal model delta harmonic sigma weight residual -180.00 -146.67 -33.33 0 5.00e+00 4.00e-02 4.44e+01 ... (remaining 9491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2024 0.059 - 0.118: 572 0.118 - 0.177: 125 0.177 - 0.237: 21 0.237 - 0.296: 12 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CB VAL E 117 " pdb=" CA VAL E 117 " pdb=" CG1 VAL E 117 " pdb=" CG2 VAL E 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2751 not shown) Planarity restraints: 2054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.020 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR F 98 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.042 2.00e-02 2.50e+03 1.76e-02 8.48e+00 pdb=" N9 DA I 39 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO A 121 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.040 5.00e-02 4.00e+02 ... (remaining 2051 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3649 2.79 - 3.32: 13286 3.32 - 3.84: 29846 3.84 - 4.37: 34463 4.37 - 4.90: 50629 Nonbonded interactions: 131873 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR L 191 " pdb=" O SER L 233 " model vdw 2.313 2.440 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.332 2.440 nonbonded pdb=" OG SER D 84 " pdb=" OP1 DG J 39 " model vdw 2.344 2.440 ... (remaining 131868 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 0.610 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: 3.730 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 53.360 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.010 0.085 16995 Z= 0.582 Angle : 1.075 12.238 24218 Z= 0.603 Chirality : 0.060 0.296 2754 Planarity : 0.007 0.073 2054 Dihedral : 26.535 178.220 7106 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.74 % Allowed : 2.04 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % Twisted Proline : 5.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.18), residues: 1238 helix: -2.45 (0.14), residues: 708 sheet: -2.33 (0.66), residues: 66 loop : -2.97 (0.23), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 600 HIS 0.007 0.002 HIS L 478 PHE 0.038 0.004 PHE L 540 TYR 0.054 0.004 TYR F 98 ARG 0.013 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 231 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 193 ASN cc_start: 0.8862 (t0) cc_final: 0.8461 (m110) REVERT: L 323 ILE cc_start: 0.8831 (mt) cc_final: 0.8607 (mp) REVERT: L 325 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7757 (tm-30) REVERT: L 327 HIS cc_start: 0.8378 (m90) cc_final: 0.7911 (m170) REVERT: L 351 ILE cc_start: 0.8221 (mt) cc_final: 0.7906 (tt) REVERT: L 470 MET cc_start: 0.8833 (tpt) cc_final: 0.8295 (tpp) REVERT: L 570 LYS cc_start: 0.8753 (mttt) cc_final: 0.8535 (tptt) REVERT: C 95 LYS cc_start: 0.9102 (tptm) cc_final: 0.8831 (tppt) REVERT: C 102 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8832 (tt) REVERT: E 42 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7272 (mmm-85) REVERT: E 50 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7346 (mm-30) REVERT: F 25 ASN cc_start: 0.5234 (m-40) cc_final: 0.4829 (m110) REVERT: H 73 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 8 outliers final: 0 residues processed: 235 average time/residue: 0.3690 time to fit residues: 119.0679 Evaluate side-chains 138 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 111 HIS L 230 GLN L 437 GLN L 477 ASN L 500 ASN L 526 GLN ** L 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 81 ASN D 106 HIS E 68 GLN H 60 ASN H 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16995 Z= 0.197 Angle : 0.658 10.383 24218 Z= 0.382 Chirality : 0.040 0.166 2754 Planarity : 0.005 0.049 2054 Dihedral : 30.516 176.225 4592 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.30 % Allowed : 8.92 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -2.34 (0.22), residues: 1238 helix: -0.81 (0.18), residues: 714 sheet: -1.86 (0.68), residues: 66 loop : -2.62 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 600 HIS 0.003 0.001 HIS L 211 PHE 0.013 0.001 PHE L 274 TYR 0.017 0.001 TYR F 98 ARG 0.006 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8708 (mt) cc_final: 0.8472 (mp) REVERT: L 351 ILE cc_start: 0.7977 (mt) cc_final: 0.7685 (tt) REVERT: L 433 MET cc_start: 0.8251 (ttm) cc_final: 0.7757 (ttt) REVERT: L 470 MET cc_start: 0.9007 (tpt) cc_final: 0.8516 (tpp) REVERT: B 63 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7682 (mt-10) REVERT: C 84 GLN cc_start: 0.9256 (tp40) cc_final: 0.8926 (tp-100) REVERT: C 95 LYS cc_start: 0.9160 (tptm) cc_final: 0.8889 (tppt) REVERT: D 58 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8894 (mt) REVERT: F 80 THR cc_start: 0.9288 (m) cc_final: 0.9063 (p) REVERT: G 90 ASP cc_start: 0.8222 (t0) cc_final: 0.8008 (t0) outliers start: 14 outliers final: 1 residues processed: 168 average time/residue: 0.3221 time to fit residues: 77.9186 Evaluate side-chains 132 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain F residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 46 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16995 Z= 0.287 Angle : 0.657 8.416 24218 Z= 0.378 Chirality : 0.040 0.167 2754 Planarity : 0.005 0.045 2054 Dihedral : 30.285 175.708 4590 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 11.34 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -1.53 (0.23), residues: 1238 helix: -0.10 (0.19), residues: 723 sheet: -1.59 (0.68), residues: 66 loop : -2.41 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 600 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE L 540 TYR 0.018 0.002 TYR F 98 ARG 0.005 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: L 277 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: L 323 ILE cc_start: 0.8607 (mt) cc_final: 0.8352 (mp) REVERT: L 351 ILE cc_start: 0.8120 (mt) cc_final: 0.7774 (tt) REVERT: L 433 MET cc_start: 0.8296 (ttm) cc_final: 0.7938 (ttt) REVERT: L 470 MET cc_start: 0.9046 (tpt) cc_final: 0.8546 (tpp) REVERT: A 120 MET cc_start: 0.8032 (mmm) cc_final: 0.7373 (mtp) REVERT: B 88 TYR cc_start: 0.8562 (m-10) cc_final: 0.8184 (m-80) REVERT: C 84 GLN cc_start: 0.9279 (tp40) cc_final: 0.8843 (tp-100) REVERT: C 95 LYS cc_start: 0.9230 (tptm) cc_final: 0.8977 (tppt) REVERT: E 54 TYR cc_start: 0.9323 (m-80) cc_final: 0.9047 (m-80) REVERT: F 34 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9035 (mt) REVERT: H 32 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7597 (mm-30) outliers start: 29 outliers final: 16 residues processed: 155 average time/residue: 0.3037 time to fit residues: 68.6693 Evaluate side-chains 142 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 277 GLN Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 277 GLN A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16995 Z= 0.240 Angle : 0.627 10.277 24218 Z= 0.363 Chirality : 0.039 0.163 2754 Planarity : 0.004 0.045 2054 Dihedral : 30.141 175.530 4590 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.79 % Allowed : 12.08 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -1.05 (0.24), residues: 1238 helix: 0.34 (0.20), residues: 717 sheet: -1.41 (0.67), residues: 66 loop : -2.26 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 600 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.001 PHE L 540 TYR 0.014 0.001 TYR F 98 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8615 (mt) cc_final: 0.8363 (mp) REVERT: L 351 ILE cc_start: 0.8096 (mt) cc_final: 0.7760 (tt) REVERT: L 433 MET cc_start: 0.8236 (ttm) cc_final: 0.7802 (ttt) REVERT: L 470 MET cc_start: 0.9015 (tpt) cc_final: 0.8551 (tpp) REVERT: B 88 TYR cc_start: 0.8524 (m-10) cc_final: 0.8175 (m-80) REVERT: C 95 LYS cc_start: 0.9221 (tptm) cc_final: 0.8966 (tppt) REVERT: E 54 TYR cc_start: 0.9329 (m-80) cc_final: 0.9018 (m-80) REVERT: E 63 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8150 (mmp80) REVERT: F 34 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9022 (mt) REVERT: F 80 THR cc_start: 0.9211 (m) cc_final: 0.8926 (p) REVERT: H 32 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7574 (mm-30) outliers start: 30 outliers final: 19 residues processed: 151 average time/residue: 0.2784 time to fit residues: 61.9717 Evaluate side-chains 146 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16995 Z= 0.196 Angle : 0.602 10.814 24218 Z= 0.349 Chirality : 0.038 0.170 2754 Planarity : 0.004 0.046 2054 Dihedral : 29.958 175.531 4590 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.16 % Allowed : 11.71 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -0.65 (0.24), residues: 1238 helix: 0.64 (0.20), residues: 728 sheet: -1.21 (0.68), residues: 66 loop : -2.11 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 600 HIS 0.003 0.001 HIS F 75 PHE 0.022 0.001 PHE L 274 TYR 0.012 0.001 TYR L 320 ARG 0.006 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8570 (mt) cc_final: 0.8259 (mp) REVERT: L 351 ILE cc_start: 0.8072 (mt) cc_final: 0.7708 (tt) REVERT: L 433 MET cc_start: 0.8215 (ttm) cc_final: 0.7687 (ttt) REVERT: L 437 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: L 470 MET cc_start: 0.9024 (tpt) cc_final: 0.8593 (tpp) REVERT: B 88 TYR cc_start: 0.8551 (m-10) cc_final: 0.8184 (m-80) REVERT: C 95 LYS cc_start: 0.9214 (tptm) cc_final: 0.8941 (tppt) REVERT: E 54 TYR cc_start: 0.9284 (m-80) cc_final: 0.8894 (m-80) REVERT: E 63 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8164 (mmp80) REVERT: F 34 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9052 (mt) REVERT: F 80 THR cc_start: 0.9216 (m) cc_final: 0.8951 (p) REVERT: H 32 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 34 outliers final: 20 residues processed: 160 average time/residue: 0.2887 time to fit residues: 68.1487 Evaluate side-chains 150 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 437 GLN Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 358 ASN L 505 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16995 Z= 0.295 Angle : 0.645 7.822 24218 Z= 0.367 Chirality : 0.040 0.175 2754 Planarity : 0.004 0.045 2054 Dihedral : 30.049 176.092 4590 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.70 % Allowed : 12.27 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -0.54 (0.24), residues: 1238 helix: 0.71 (0.20), residues: 731 sheet: -1.16 (0.67), residues: 67 loop : -2.05 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 600 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE L 540 TYR 0.013 0.002 TYR F 98 ARG 0.004 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8501 (mt) cc_final: 0.8192 (mp) REVERT: L 351 ILE cc_start: 0.8130 (mt) cc_final: 0.7713 (tt) REVERT: L 470 MET cc_start: 0.9039 (tpt) cc_final: 0.8632 (tpp) REVERT: A 120 MET cc_start: 0.8016 (mmm) cc_final: 0.7507 (mtp) REVERT: B 88 TYR cc_start: 0.8586 (m-10) cc_final: 0.8311 (m-80) REVERT: C 95 LYS cc_start: 0.9200 (tptm) cc_final: 0.8910 (tppt) REVERT: E 54 TYR cc_start: 0.9296 (m-80) cc_final: 0.8890 (m-80) REVERT: E 63 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8242 (mmp80) REVERT: E 97 GLU cc_start: 0.7935 (tt0) cc_final: 0.7666 (mt-10) REVERT: F 34 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9095 (mt) REVERT: F 80 THR cc_start: 0.9198 (m) cc_final: 0.8885 (p) REVERT: G 36 LYS cc_start: 0.8833 (tppp) cc_final: 0.8589 (ttmm) REVERT: H 32 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7675 (mm-30) outliers start: 29 outliers final: 23 residues processed: 142 average time/residue: 0.2848 time to fit residues: 60.5244 Evaluate side-chains 142 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain L residue 530 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 505 GLN A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16995 Z= 0.171 Angle : 0.593 10.172 24218 Z= 0.341 Chirality : 0.036 0.170 2754 Planarity : 0.004 0.045 2054 Dihedral : 29.688 176.894 4590 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -0.28 (0.25), residues: 1238 helix: 0.90 (0.20), residues: 737 sheet: -1.05 (0.67), residues: 68 loop : -1.96 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 260 HIS 0.003 0.001 HIS B 18 PHE 0.017 0.001 PHE E 67 TYR 0.008 0.001 TYR L 191 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8439 (mt) cc_final: 0.8150 (mp) REVERT: L 351 ILE cc_start: 0.8090 (mt) cc_final: 0.7710 (tt) REVERT: L 433 MET cc_start: 0.7952 (ttm) cc_final: 0.7612 (ttt) REVERT: B 84 MET cc_start: 0.7654 (tpp) cc_final: 0.7328 (tpt) REVERT: B 88 TYR cc_start: 0.8601 (m-10) cc_final: 0.8210 (m-80) REVERT: C 18 SER cc_start: 0.9039 (m) cc_final: 0.8738 (t) REVERT: C 50 TYR cc_start: 0.9009 (t80) cc_final: 0.8781 (t80) REVERT: E 54 TYR cc_start: 0.9262 (m-80) cc_final: 0.8800 (m-80) REVERT: E 63 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8151 (mmp80) REVERT: E 97 GLU cc_start: 0.7895 (tt0) cc_final: 0.7695 (mt-10) REVERT: E 124 ILE cc_start: 0.9078 (tt) cc_final: 0.8877 (tt) REVERT: F 80 THR cc_start: 0.9211 (m) cc_final: 0.9002 (p) REVERT: G 36 LYS cc_start: 0.8820 (tppp) cc_final: 0.8584 (ttmm) REVERT: H 32 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7589 (mm-30) outliers start: 18 outliers final: 11 residues processed: 155 average time/residue: 0.2956 time to fit residues: 67.1629 Evaluate side-chains 141 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 437 GLN L 505 GLN A 93 GLN B 25 ASN E 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16995 Z= 0.246 Angle : 0.618 9.612 24218 Z= 0.351 Chirality : 0.038 0.163 2754 Planarity : 0.004 0.042 2054 Dihedral : 29.831 177.162 4590 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.95 % Allowed : 14.50 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: -0.08 (0.25), residues: 1238 helix: 1.06 (0.20), residues: 729 sheet: -0.85 (0.66), residues: 67 loop : -1.83 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 600 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.001 PHE L 540 TYR 0.013 0.001 TYR F 51 ARG 0.003 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8380 (mt) cc_final: 0.8043 (mp) REVERT: L 351 ILE cc_start: 0.7898 (mt) cc_final: 0.7477 (tt) REVERT: L 433 MET cc_start: 0.8057 (ttm) cc_final: 0.7821 (ttt) REVERT: L 470 MET cc_start: 0.8717 (tpt) cc_final: 0.8269 (tpp) REVERT: B 84 MET cc_start: 0.7614 (tpp) cc_final: 0.7257 (tpt) REVERT: B 88 TYR cc_start: 0.8612 (m-10) cc_final: 0.8204 (m-80) REVERT: C 18 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8806 (t) REVERT: E 42 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7871 (tpt90) REVERT: E 54 TYR cc_start: 0.9266 (m-80) cc_final: 0.8811 (m-80) REVERT: E 63 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8250 (mmp80) REVERT: E 97 GLU cc_start: 0.7889 (tt0) cc_final: 0.7672 (mt-10) REVERT: F 80 THR cc_start: 0.9159 (m) cc_final: 0.8852 (p) REVERT: G 36 LYS cc_start: 0.8829 (tppp) cc_final: 0.8591 (ttmm) REVERT: H 32 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7596 (mm-30) outliers start: 21 outliers final: 16 residues processed: 139 average time/residue: 0.2868 time to fit residues: 59.0461 Evaluate side-chains 137 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 505 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16995 Z= 0.230 Angle : 0.608 10.088 24218 Z= 0.346 Chirality : 0.037 0.163 2754 Planarity : 0.004 0.043 2054 Dihedral : 29.720 177.229 4590 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.86 % Allowed : 14.50 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.00 (0.25), residues: 1238 helix: 1.09 (0.20), residues: 730 sheet: -0.67 (0.66), residues: 67 loop : -1.75 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 600 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE L 540 TYR 0.010 0.001 TYR F 98 ARG 0.003 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 2.239 Fit side-chains revert: symmetry clash REVERT: L 323 ILE cc_start: 0.8367 (mt) cc_final: 0.8038 (mp) REVERT: L 351 ILE cc_start: 0.8039 (mt) cc_final: 0.7641 (tt) REVERT: L 433 MET cc_start: 0.7970 (ttm) cc_final: 0.7739 (ttt) REVERT: L 470 MET cc_start: 0.8701 (tpt) cc_final: 0.8267 (tpp) REVERT: B 84 MET cc_start: 0.7631 (tpp) cc_final: 0.7276 (tpt) REVERT: B 88 TYR cc_start: 0.8597 (m-10) cc_final: 0.8197 (m-80) REVERT: C 18 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8816 (t) REVERT: E 54 TYR cc_start: 0.9261 (m-80) cc_final: 0.8800 (m-80) REVERT: E 63 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8245 (mmp80) REVERT: E 97 GLU cc_start: 0.7876 (tt0) cc_final: 0.7661 (mt-10) REVERT: F 80 THR cc_start: 0.9161 (m) cc_final: 0.8871 (p) REVERT: G 36 LYS cc_start: 0.8832 (tppp) cc_final: 0.8591 (ttmm) REVERT: H 32 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7648 (mm-30) outliers start: 20 outliers final: 17 residues processed: 132 average time/residue: 0.3008 time to fit residues: 59.3906 Evaluate side-chains 134 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 GLN A 93 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16995 Z= 0.212 Angle : 0.600 10.870 24218 Z= 0.341 Chirality : 0.036 0.164 2754 Planarity : 0.004 0.043 2054 Dihedral : 29.650 177.270 4590 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 14.87 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.15 (0.25), residues: 1238 helix: 1.15 (0.20), residues: 729 sheet: -0.61 (0.67), residues: 68 loop : -1.56 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 600 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.008 0.001 TYR L 191 ARG 0.003 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: L 470 MET cc_start: 0.8708 (tpt) cc_final: 0.8276 (tpp) REVERT: B 84 MET cc_start: 0.7622 (tpp) cc_final: 0.7263 (tpt) REVERT: B 88 TYR cc_start: 0.8585 (m-10) cc_final: 0.8189 (m-80) REVERT: C 18 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8815 (t) REVERT: E 42 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7881 (tpt90) REVERT: E 54 TYR cc_start: 0.9246 (m-80) cc_final: 0.8775 (m-80) REVERT: E 63 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8254 (mmp80) REVERT: E 97 GLU cc_start: 0.7859 (tt0) cc_final: 0.7656 (mt-10) REVERT: F 80 THR cc_start: 0.9146 (m) cc_final: 0.8877 (p) REVERT: G 36 LYS cc_start: 0.8835 (tppp) cc_final: 0.8589 (ttmm) REVERT: H 32 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7624 (mm-30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.2821 time to fit residues: 55.7109 Evaluate side-chains 133 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 577 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 505 GLN A 93 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.087359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058887 restraints weight = 58574.160| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.48 r_work: 0.2843 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16995 Z= 0.228 Angle : 0.605 10.772 24218 Z= 0.343 Chirality : 0.037 0.166 2754 Planarity : 0.004 0.041 2054 Dihedral : 29.642 177.293 4590 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.95 % Allowed : 14.96 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.08 % 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: 0.22 (0.25), residues: 1238 helix: 1.19 (0.20), residues: 725 sheet: -0.57 (0.63), residues: 78 loop : -1.51 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 600 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.012 0.001 TYR F 98 ARG 0.002 0.000 ARG L 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.90 seconds wall clock time: 52 minutes 59.84 seconds (3179.84 seconds total)