Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 09:21:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srs_25403/04_2023/7srs_25403_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srs_25403/04_2023/7srs_25403.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/7srs_25403/04_2023/7srs_25403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srs_25403/04_2023/7srs_25403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srs_25403/04_2023/7srs_25403_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7srs_25403/04_2023/7srs_25403_neut_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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3682 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 36 5.16 5 C 5406 2.51 5 N 1381 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8361 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 768 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 959 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2234 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2682 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 326} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 893 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'7LD': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8361 At special positions: 0 Unit cell: (99.6957, 92.0268, 175.533, 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 36 16.00 P 3 15.00 O 1535 8.00 N 1381 7.00 C 5406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 87 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " distance=2.03 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 204 " Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 18 sheets defined 23.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'R' and resid 57 through 81 removed outlier: 3.612A pdb=" N VAL R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 88 through 116 removed outlier: 4.492A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 125 through 158 Proline residue: R 129 - end of helix removed outlier: 3.519A pdb=" N LYS R 158 " --> pdb=" O ILE R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 166 Processing helix chain 'R' and resid 169 through 192 Proline residue: R 189 - end of helix removed outlier: 4.414A pdb=" N ILE R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 211 through 225 removed outlier: 6.600A pdb=" N ASP R 216 " --> pdb=" O GLU R 212 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 250 removed outlier: 3.512A pdb=" N ILE R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 349 Proline residue: R 339 - end of helix Processing helix chain 'R' and resid 355 through 382 removed outlier: 3.528A pdb=" N ILE R 364 " --> pdb=" O MET R 360 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE R 368 " --> pdb=" O ILE R 364 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY R 369 " --> pdb=" O PHE R 365 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY R 374 " --> pdb=" O TYR R 370 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.683A pdb=" N TYR R 380 " --> pdb=" O ASN R 376 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 396 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.623A pdb=" N VAL P 19 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.510A pdb=" N LYS P 102 " --> pdb=" O MET P 11 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA P 13 " --> pdb=" O LYS P 102 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU P 104 " --> pdb=" O ALA P 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'P' and resid 84 through 89 removed outlier: 5.798A pdb=" N GLN P 36 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU P 45 " --> pdb=" O GLN P 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id= E, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id= F, first strand: chain 'Q' and resid 93 through 97 removed outlier: 3.764A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TRP Q 47 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Q' and resid 101 through 104 removed outlier: 3.568A pdb=" N SER Q 101 " --> pdb=" O ASN Q 112 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= I, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.520A pdb=" N GLU C 169 " --> pdb=" O PHE C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 75 through 78 removed outlier: 3.546A pdb=" N ARG C 62 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 183 through 189 Processing sheet with id= L, first strand: chain 'C' and resid 334 through 341 removed outlier: 3.878A pdb=" N PHE C 341 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR C 321 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 254 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 241 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN C 248 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 53 through 59 removed outlier: 4.018A pdb=" N PHE C 87 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.869A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.634A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= Q, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.571A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.509A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 912 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: 2.58 Time building geometry restraints manager: 3.37 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: 2602 1.34 - 1.47: 2163 1.47 - 1.59: 3738 1.59 - 1.71: 12 1.71 - 1.83: 52 Bond restraints: 8567 Sorted by residual: bond pdb=" C14 7LD R 502 " pdb=" C16 7LD R 502 " ideal model delta sigma weight residual 1.525 1.403 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C11 7LD R 502 " pdb=" C9 7LD R 502 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C10 7LD R 502 " pdb=" C14 7LD R 502 " ideal model delta sigma weight residual 1.501 1.397 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C15 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.414 1.321 0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.02: 230 106.02 - 113.03: 4749 113.03 - 120.04: 2728 120.04 - 127.05: 3891 127.05 - 134.05: 109 Bond angle restraints: 11707 Sorted by residual: angle pdb=" CA GLU C 134 " pdb=" C GLU C 134 " pdb=" O GLU C 134 " ideal model delta sigma weight residual 120.90 117.55 3.35 1.03e+00 9.43e-01 1.06e+01 angle pdb=" C LYS C 138 " pdb=" CA LYS C 138 " pdb=" CB LYS C 138 " ideal model delta sigma weight residual 114.40 110.64 3.76 1.25e+00 6.40e-01 9.04e+00 angle pdb=" CA LYS R 324 " pdb=" C LYS R 324 " pdb=" O LYS R 324 " ideal model delta sigma weight residual 120.82 117.86 2.96 1.05e+00 9.07e-01 7.96e+00 angle pdb=" C GLY P 67 " pdb=" N THR P 68 " pdb=" CA THR P 68 " ideal model delta sigma weight residual 122.19 126.01 -3.82 1.41e+00 5.03e-01 7.34e+00 angle pdb=" C MET R 336 " pdb=" N TRP R 337 " pdb=" CA TRP R 337 " ideal model delta sigma weight residual 122.54 118.25 4.29 1.65e+00 3.67e-01 6.76e+00 ... (remaining 11702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 4917 30.35 - 60.70: 109 60.70 - 91.05: 12 91.05 - 121.40: 0 121.40 - 151.75: 1 Dihedral angle restraints: 5039 sinusoidal: 1820 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS R 128 " pdb=" SG CYS R 128 " pdb=" SG CYS R 207 " pdb=" CB CYS R 207 " ideal model delta sinusoidal sigma weight residual -86.00 -157.82 71.82 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" C16 7LD R 502 " pdb=" C17 7LD R 502 " pdb=" N3 7LD R 502 " pdb=" C18 7LD R 502 " ideal model delta sinusoidal sigma weight residual 91.75 -116.50 -151.75 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA ARG C 307 " pdb=" C ARG C 307 " pdb=" N GLU C 308 " pdb=" CA GLU C 308 " ideal model delta harmonic sigma weight residual -180.00 -158.88 -21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1190 0.066 - 0.132: 173 0.132 - 0.198: 8 0.198 - 0.264: 0 0.264 - 0.329: 3 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C14 7LD R 502 " pdb=" C10 7LD R 502 " pdb=" C13 7LD R 502 " pdb=" C16 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C11 7LD R 502 " pdb=" C15 7LD R 502 " pdb=" C9 7LD R 502 " pdb=" N2 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 204 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1371 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 357 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 358 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 275 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO C 276 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 276 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 276 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 113 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO C 114 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 114 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 114 " 0.020 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1540 2.77 - 3.31: 7170 3.31 - 3.84: 12320 3.84 - 4.37: 13482 4.37 - 4.90: 25929 Nonbonded interactions: 60441 Sorted by model distance: nonbonded pdb=" OD2 ASP C 29 " pdb=" NZ LYS C 170 " model vdw 2.242 2.520 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.290 2.440 nonbonded pdb=" OG SER P 7 " pdb=" OG1 THR P 22 " model vdw 2.356 2.440 nonbonded pdb=" O GLN R 320 " pdb=" OG SER R 323 " model vdw 2.375 2.440 nonbonded pdb=" O LEU R 85 " pdb=" ND2 ASN R 90 " model vdw 2.400 2.520 ... (remaining 60436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 8.950 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 24.520 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.005 0.122 8567 Z= 0.352 Angle : 0.664 6.126 11707 Z= 0.369 Chirality : 0.046 0.329 1374 Planarity : 0.005 0.079 1458 Dihedral : 12.770 151.751 2955 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.87 (0.25), residues: 1082 helix: 2.91 (0.33), residues: 238 sheet: 0.97 (0.26), residues: 403 loop : -1.17 (0.26), residues: 441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.008 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.2397 time to fit residues: 43.1326 Evaluate side-chains 111 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 ASN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8567 Z= 0.259 Angle : 0.583 6.565 11707 Z= 0.312 Chirality : 0.044 0.232 1374 Planarity : 0.005 0.060 1458 Dihedral : 6.940 154.737 1199 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1082 helix: 2.45 (0.33), residues: 236 sheet: 0.93 (0.25), residues: 403 loop : -1.22 (0.26), residues: 443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.017 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 124 average time/residue: 0.2291 time to fit residues: 38.2686 Evaluate side-chains 123 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0817 time to fit residues: 3.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 376 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 8567 Z= 0.389 Angle : 0.649 6.716 11707 Z= 0.346 Chirality : 0.046 0.209 1374 Planarity : 0.005 0.055 1458 Dihedral : 7.273 163.677 1199 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.31 (0.25), residues: 1082 helix: 2.09 (0.34), residues: 237 sheet: 0.76 (0.26), residues: 400 loop : -1.42 (0.25), residues: 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.067 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.2255 time to fit residues: 38.0857 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1184 time to fit residues: 3.1049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8567 Z= 0.235 Angle : 0.567 6.545 11707 Z= 0.301 Chirality : 0.043 0.207 1374 Planarity : 0.005 0.050 1458 Dihedral : 7.121 164.062 1199 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.39 (0.25), residues: 1082 helix: 2.21 (0.35), residues: 234 sheet: 0.80 (0.26), residues: 401 loop : -1.37 (0.25), residues: 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.021 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.2224 time to fit residues: 36.0047 Evaluate side-chains 115 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0793 time to fit residues: 3.0588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 0.0030 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8567 Z= 0.247 Angle : 0.571 6.398 11707 Z= 0.301 Chirality : 0.043 0.200 1374 Planarity : 0.005 0.049 1458 Dihedral : 7.106 165.550 1199 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.43 (0.25), residues: 1082 helix: 2.20 (0.35), residues: 235 sheet: 0.85 (0.25), residues: 406 loop : -1.39 (0.26), residues: 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.121 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.2424 time to fit residues: 36.1080 Evaluate side-chains 106 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1633 time to fit residues: 2.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 8567 Z= 0.433 Angle : 0.685 7.123 11707 Z= 0.363 Chirality : 0.047 0.178 1374 Planarity : 0.005 0.050 1458 Dihedral : 7.585 173.553 1199 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 1082 helix: 1.87 (0.35), residues: 235 sheet: 0.79 (0.26), residues: 387 loop : -1.63 (0.25), residues: 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.075 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 123 average time/residue: 0.2171 time to fit residues: 36.8066 Evaluate side-chains 121 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0777 time to fit residues: 3.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8567 Z= 0.205 Angle : 0.566 6.996 11707 Z= 0.298 Chirality : 0.043 0.185 1374 Planarity : 0.005 0.049 1458 Dihedral : 7.199 167.768 1199 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.32 (0.25), residues: 1082 helix: 2.15 (0.36), residues: 234 sheet: 0.87 (0.26), residues: 394 loop : -1.51 (0.25), residues: 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.897 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 117 average time/residue: 0.2365 time to fit residues: 37.3012 Evaluate side-chains 110 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0965 time to fit residues: 2.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8567 Z= 0.335 Angle : 0.636 7.548 11707 Z= 0.332 Chirality : 0.045 0.176 1374 Planarity : 0.005 0.049 1458 Dihedral : 7.336 170.380 1199 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.19 (0.25), residues: 1082 helix: 2.03 (0.36), residues: 235 sheet: 0.84 (0.26), residues: 388 loop : -1.59 (0.25), residues: 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 113 average time/residue: 0.2610 time to fit residues: 39.7518 Evaluate side-chains 114 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0805 time to fit residues: 2.0978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8567 Z= 0.170 Angle : 0.551 7.784 11707 Z= 0.285 Chirality : 0.042 0.168 1374 Planarity : 0.004 0.050 1458 Dihedral : 6.991 164.715 1199 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.41 (0.25), residues: 1082 helix: 2.24 (0.36), residues: 234 sheet: 0.95 (0.26), residues: 397 loop : -1.51 (0.26), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.062 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2393 time to fit residues: 36.6107 Evaluate side-chains 105 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 0.0000 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8567 Z= 0.174 Angle : 0.550 7.933 11707 Z= 0.284 Chirality : 0.042 0.167 1374 Planarity : 0.004 0.051 1458 Dihedral : 6.911 162.912 1199 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.46 (0.26), residues: 1082 helix: 2.25 (0.36), residues: 235 sheet: 1.06 (0.26), residues: 393 loop : -1.52 (0.26), residues: 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.2268 time to fit residues: 33.5336 Evaluate side-chains 107 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0814 time to fit residues: 1.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080815 restraints weight = 16597.784| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.29 r_work: 0.3015 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8567 Z= 0.224 Angle : 0.582 7.900 11707 Z= 0.301 Chirality : 0.043 0.163 1374 Planarity : 0.004 0.051 1458 Dihedral : 6.953 162.666 1199 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.56 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.10 % 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: 0.41 (0.26), residues: 1082 helix: 2.20 (0.36), residues: 235 sheet: 1.03 (0.26), residues: 391 loop : -1.54 (0.26), residues: 456 =============================================================================== Job complete usr+sys time: 1993.39 seconds wall clock time: 36 minutes 40.06 seconds (2200.06 seconds total)