Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:47:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yet_33777/02_2023/7yet_33777_updated.pdb" } resolution = 3.3 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= 0.002 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 "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11862 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 8038 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 4 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: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} 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: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'SVR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'SVR:plan-7': 1, 'SVR:plan-4': 1, 'SVR:plan-3': 1, 'SVR:plan-9': 1} Unresolved non-hydrogen planarities: 31 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 7.81, per 1000 atoms: 0.66 Number of scatterers: 11862 At special positions: 0 Unit cell: (177.84, 132.08, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2227 8.00 N 1981 7.00 C 7588 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: 4.70 Conformation dependent library (CDL) restraints added in 2.1 seconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 5 sheets defined 53.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.881A pdb=" N THR A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.605A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.533A pdb=" N ASP A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.664A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 217 through 220 No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 236 through 260 removed outlier: 3.719A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 307 removed outlier: 7.499A pdb=" N SER A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 318 through 333 Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.897A pdb=" N SER A 370 " --> pdb=" O CYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.620A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 568 through 583 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.875A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 713 through 730 Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.592A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.569A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG A 821 " --> pdb=" O LYS A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 821' Processing helix chain 'A' and resid 833 through 849 Processing helix chain 'A' and resid 855 through 874 removed outlier: 3.714A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 917 through 920 Processing helix chain 'A' and resid 928 through 942 Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 964 through 967 No H-bonds generated for 'chain 'A' and resid 964 through 967' Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 1070 through 1084 Processing helix chain 'A' and resid 1316 through 1330 removed outlier: 3.937A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 147 removed outlier: 3.959A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Proline residue: B 120 - end of helix removed outlier: 3.586A pdb=" N ASP B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.547A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 4.263A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.853A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'C' and resid 82 through 117 Processing helix chain 'C' and resid 121 through 143 removed outlier: 3.739A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'D' and resid 83 through 111 Processing helix chain 'D' and resid 115 through 145 Proline residue: D 120 - end of helix removed outlier: 4.028A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 145 removed outlier: 4.842A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.717A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 172 through 177 Processing sheet with id= B, first strand: chain 'A' and resid 549 through 552 Processing sheet with id= C, first strand: chain 'A' and resid 626 through 632 removed outlier: 3.819A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 799 through 801 Processing sheet with id= E, first strand: chain 'B' and resid 293 through 297 removed outlier: 6.968A pdb=" N LEU B 338 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL B 327 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU B 336 " --> pdb=" O VAL B 327 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3803 1.34 - 1.46: 2046 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12138 Sorted by residual: bond pdb=" O25 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.469 1.566 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O30 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.472 1.566 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 SVR A2301 " pdb=" C20 SVR A2301 " ideal model delta sigma weight residual 1.401 1.482 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O24 SVR A2301 " pdb=" S17 SVR A2301 " ideal model delta sigma weight residual 1.485 1.429 0.056 2.00e-02 2.50e+03 7.84e+00 bond pdb=" O29 SVR A2301 " pdb=" S21 SVR A2301 " ideal model delta sigma weight residual 1.473 1.418 0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.88: 216 104.88 - 112.16: 6157 112.16 - 119.44: 3974 119.44 - 126.72: 5993 126.72 - 134.00: 171 Bond angle restraints: 16511 Sorted by residual: angle pdb=" N ILE A 963 " pdb=" CA ILE A 963 " pdb=" C ILE A 963 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N PHE A 113 " pdb=" CA PHE A 113 " pdb=" C PHE A 113 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N ASN A 87 " pdb=" CA ASN A 87 " pdb=" C ASN A 87 " ideal model delta sigma weight residual 114.75 110.40 4.35 1.26e+00 6.30e-01 1.19e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N GLN B 100 " pdb=" CA GLN B 100 " pdb=" CB GLN B 100 " ideal model delta sigma weight residual 110.28 115.23 -4.95 1.55e+00 4.16e-01 1.02e+01 ... (remaining 16506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6551 17.89 - 35.79: 587 35.79 - 53.68: 108 53.68 - 71.57: 25 71.57 - 89.46: 7 Dihedral angle restraints: 7278 sinusoidal: 2872 harmonic: 4406 Sorted by residual: dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual 180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1484 0.047 - 0.093: 322 0.093 - 0.139: 70 0.139 - 0.186: 3 0.186 - 0.232: 1 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA GLN B 99 " pdb=" N GLN B 99 " pdb=" C GLN B 99 " pdb=" CB GLN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1877 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 SVR A2301 " 0.316 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C26 SVR A2301 " -0.092 2.00e-02 2.50e+03 pdb=" C33 SVR A2301 " 0.194 2.00e-02 2.50e+03 pdb=" N19 SVR A2301 " -0.437 2.00e-02 2.50e+03 pdb=" O32 SVR A2301 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 SVR A2301 " 0.235 2.00e-02 2.50e+03 2.33e-01 8.17e+02 pdb=" C43 SVR A2301 " -0.016 2.00e-02 2.50e+03 pdb=" C46 SVR A2301 " -0.146 2.00e-02 2.50e+03 pdb=" N41 SVR A2301 " -0.335 2.00e-02 2.50e+03 pdb=" N44 SVR A2301 " 0.359 2.00e-02 2.50e+03 pdb=" O45 SVR A2301 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 SVR A2301 " 0.050 2.00e-02 2.50e+03 1.96e-01 4.80e+02 pdb=" C3 SVR A2301 " -0.229 2.00e-02 2.50e+03 pdb=" C5 SVR A2301 " 0.010 2.00e-02 2.50e+03 pdb=" N1 SVR A2301 " 0.332 2.00e-02 2.50e+03 pdb=" O4 SVR A2301 " -0.163 2.00e-02 2.50e+03 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1160 2.74 - 3.28: 12036 3.28 - 3.82: 19617 3.82 - 4.36: 22118 4.36 - 4.90: 39221 Nonbonded interactions: 94152 Sorted by model distance: nonbonded pdb=" OG1 THR A 70 " pdb=" O VAL A 229 " model vdw 2.204 2.440 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 690 " model vdw 2.217 2.440 nonbonded pdb=" OD2 ASP A 20 " pdb=" ND2 ASN A 681 " model vdw 2.287 2.520 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.302 2.440 ... (remaining 94147 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 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7588 2.51 5 N 1981 2.21 5 O 2227 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.190 Process input model: 33.950 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.004 0.097 12138 Z= 0.223 Angle : 0.612 8.382 16511 Z= 0.318 Chirality : 0.039 0.232 1880 Planarity : 0.010 0.260 2111 Dihedral : 14.412 89.464 4422 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.90 % Favored : 93.69 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1487 helix: 2.07 (0.19), residues: 837 sheet: 0.65 (0.55), residues: 73 loop : -0.94 (0.27), residues: 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.426 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.2510 time to fit residues: 67.9201 Evaluate side-chains 148 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 12138 Z= 0.246 Angle : 0.613 15.506 16511 Z= 0.297 Chirality : 0.040 0.155 1880 Planarity : 0.005 0.077 2111 Dihedral : 4.794 72.463 1615 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.90 % Favored : 93.63 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1487 helix: 2.14 (0.19), residues: 836 sheet: 0.77 (0.55), residues: 73 loop : -1.08 (0.27), residues: 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.288 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 162 average time/residue: 0.2646 time to fit residues: 61.7089 Evaluate side-chains 154 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1072 time to fit residues: 4.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 978 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12138 Z= 0.224 Angle : 0.592 15.023 16511 Z= 0.286 Chirality : 0.040 0.195 1880 Planarity : 0.004 0.072 2111 Dihedral : 4.679 65.103 1615 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.17 % Favored : 93.42 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1487 helix: 2.15 (0.19), residues: 837 sheet: 0.75 (0.54), residues: 73 loop : -1.07 (0.27), residues: 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.476 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 161 average time/residue: 0.2663 time to fit residues: 61.6050 Evaluate side-chains 145 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1091 time to fit residues: 2.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: