Starting phenix.real_space_refine (version: dev) on Wed Feb 22 00:24:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/02_2023/6iro_9720_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/02_2023/6iro_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_9720/02_2023/6iro_9720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/02_2023/6iro_9720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/02_2023/6iro_9720_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iro_9720/02_2023/6iro_9720_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.42, 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: 7.55 Conformation dependent library (CDL) restraints added in 1.5 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: 6.24 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: 7.04 Time building geometry restraints manager: 8.01 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 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 angle pdb=" C LEU L 405 " pdb=" N GLN L 406 " pdb=" CA GLN L 406 " ideal model delta sigma weight residual 120.06 125.18 -5.12 1.19e+00 7.06e-01 1.85e+01 ... (remaining 24213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7772 35.64 - 71.29: 1405 71.29 - 106.93: 50 106.93 - 142.58: 4 142.58 - 178.22: 7 Dihedral angle restraints: 9238 sinusoidal: 5553 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 9235 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 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. 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: 1.170 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: 0.030 Extract box with map and model: 4.420 Check model and map are aligned: 0.240 Process input model: 49.100 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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= 0.602 Chirality : 0.060 0.296 2754 Planarity : 0.007 0.073 2054 Dihedral : 26.342 178.220 6850 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 % 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 *********************** 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 : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 235 average time/residue: 0.3723 time to fit residues: 118.9333 Evaluate side-chains 131 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 81 ASN D 106 HIS E 68 GLN H 44 GLN H 60 ASN H 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 16995 Z= 0.191 Angle : 0.663 12.632 24218 Z= 0.383 Chirality : 0.040 0.172 2754 Planarity : 0.005 0.049 2054 Dihedral : 30.750 177.351 4334 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.30 % 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: -2.39 (0.21), residues: 1238 helix: -0.85 (0.18), residues: 716 sheet: -1.84 (0.68), residues: 66 loop : -2.64 (0.24), residues: 456 *********************** 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 171 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.494 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 167 average time/residue: 0.3091 time to fit residues: 74.4040 Evaluate side-chains 127 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1330 time to fit residues: 2.3176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 277 GLN B 93 GLN D 46 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 16995 Z= 0.389 Angle : 0.719 12.116 24218 Z= 0.406 Chirality : 0.043 0.170 2754 Planarity : 0.005 0.045 2054 Dihedral : 30.823 177.279 4334 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 2.97 % 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: -1.71 (0.23), residues: 1238 helix: -0.27 (0.19), residues: 726 sheet: -1.65 (0.67), residues: 66 loop : -2.45 (0.26), residues: 446 *********************** 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 161 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.615 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 152 average time/residue: 0.3050 time to fit residues: 67.8508 Evaluate side-chains 137 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1376 time to fit residues: 6.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16995 Z= 0.186 Angle : 0.601 12.346 24218 Z= 0.348 Chirality : 0.038 0.173 2754 Planarity : 0.004 0.048 2054 Dihedral : 30.282 176.375 4334 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.77 % 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: -0.99 (0.24), residues: 1238 helix: 0.36 (0.20), residues: 727 sheet: -1.33 (0.67), residues: 66 loop : -2.24 (0.26), residues: 445 *********************** 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 165 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 158 average time/residue: 0.3088 time to fit residues: 71.0739 Evaluate side-chains 135 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1422 time to fit residues: 4.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 205 ASN L 277 GLN L 358 ASN L 505 GLN A 93 GLN B 25 ASN B 93 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 16995 Z= 0.372 Angle : 0.683 12.088 24218 Z= 0.384 Chirality : 0.041 0.175 2754 Planarity : 0.005 0.043 2054 Dihedral : 30.532 176.672 4334 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.49 % 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: -0.91 (0.24), residues: 1238 helix: 0.41 (0.20), residues: 730 sheet: -1.21 (0.68), residues: 66 loop : -2.22 (0.26), residues: 442 *********************** 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 133 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.654 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.3272 time to fit residues: 62.0655 Evaluate side-chains 122 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1551 time to fit residues: 4.3209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 overall best weight: 2.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 205 ASN L 505 GLN A 93 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3262 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= 0.294 Angle : 0.653 12.063 24218 Z= 0.369 Chirality : 0.040 0.164 2754 Planarity : 0.004 0.043 2054 Dihedral : 30.445 176.913 4334 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.12 % 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: -0.75 (0.24), residues: 1238 helix: 0.49 (0.20), residues: 738 sheet: -1.09 (0.67), residues: 67 loop : -2.13 (0.27), residues: 433 *********************** 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 127 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.661 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.3193 time to fit residues: 58.6483 Evaluate side-chains 119 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1426 time to fit residues: 3.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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: 0.8435 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16995 Z= 0.176 Angle : 0.594 12.314 24218 Z= 0.339 Chirality : 0.036 0.159 2754 Planarity : 0.004 0.042 2054 Dihedral : 29.989 177.892 4334 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.37 % 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: -0.94 (0.67), residues: 68 loop : -1.96 (0.28), residues: 433 *********************** 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 152 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.471 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 151 average time/residue: 0.2900 time to fit residues: 65.4287 Evaluate side-chains 129 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1817 time to fit residues: 2.1740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 477 ASN L 505 GLN B 25 ASN C 84 GLN E 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16995 Z= 0.176 Angle : 0.586 12.344 24218 Z= 0.331 Chirality : 0.036 0.194 2754 Planarity : 0.004 0.046 2054 Dihedral : 29.875 177.229 4334 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.02 % 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: 0.09 (0.25), residues: 1238 helix: 1.18 (0.20), residues: 728 sheet: -0.78 (0.67), residues: 68 loop : -1.72 (0.28), residues: 442 *********************** 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 148 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.510 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 0.3004 time to fit residues: 63.7465 Evaluate side-chains 128 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1464 time to fit residues: 3.4173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 120 optimal weight: 0.0970 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3974 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= 0.241 Angle : 0.615 12.252 24218 Z= 0.346 Chirality : 0.037 0.164 2754 Planarity : 0.004 0.043 2054 Dihedral : 29.883 177.529 4334 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.65 % 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: 0.13 (0.25), residues: 1238 helix: 1.17 (0.20), residues: 725 sheet: -0.67 (0.66), residues: 68 loop : -1.63 (0.28), residues: 445 *********************** 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 130 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.518 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.3109 time to fit residues: 58.6241 Evaluate side-chains 124 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1562 time to fit residues: 2.9380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16995 Z= 0.200 Angle : 0.606 12.224 24218 Z= 0.339 Chirality : 0.036 0.161 2754 Planarity : 0.004 0.043 2054 Dihedral : 29.798 177.077 4334 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.00 % 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: 0.23 (0.25), residues: 1238 helix: 1.21 (0.20), residues: 730 sheet: -0.47 (0.68), residues: 67 loop : -1.56 (0.28), residues: 441 ********************** 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 125 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.482 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3092 time to fit residues: 57.3038 Evaluate side-chains 123 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 205 ASN ** L 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 505 GLN A 93 GLN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.085422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056165 restraints weight = 58829.219| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.41 r_work: 0.2781 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 16995 Z= 0.394 Angle : 0.697 12.117 24218 Z= 0.388 Chirality : 0.041 0.175 2754 Planarity : 0.005 0.044 2054 Dihedral : 30.159 176.932 4334 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.65 % 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: -0.06 (0.24), residues: 1238 helix: 0.93 (0.20), residues: 725 sheet: -0.44 (0.68), residues: 66 loop : -1.58 (0.28), residues: 447 =============================================================================== Job complete usr+sys time: 2681.24 seconds wall clock time: 49 minutes 32.53 seconds (2972.53 seconds total)