Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 04:52:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/10_2023/7kjx_22901_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 5398 2.51 5 N 1453 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4359 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 508} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3269 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 29, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'DNA': 1, 'RNA': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MG': 1, 'NVP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.31, per 1000 atoms: 0.62 Number of scatterers: 8589 At special positions: 0 Unit cell: (77.9, 106.6, 118.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 44 15.00 Mg 1 11.99 O 1679 8.00 N 1453 7.00 C 5398 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 34.9% alpha, 13.4% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 154 through 174 removed outlier: 4.792A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.724A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.921A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.664A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.974A pdb=" N LEU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.642A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.833A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.708A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.670A pdb=" N PHE B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 4.529A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 128' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.855A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.846A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.068A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.673A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 401 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.597A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 63 Processing sheet with id= C, first strand: chain 'A' and resid 179 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= E, first strand: chain 'A' and resid 326 through 331 Processing sheet with id= F, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= G, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.842A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 457 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= I, first strand: chain 'B' and resid 60 through 64 Processing sheet with id= J, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= K, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.857A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 4.32 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: 2443 1.34 - 1.46: 1780 1.46 - 1.58: 4573 1.58 - 1.69: 86 1.69 - 1.81: 24 Bond restraints: 8906 Sorted by residual: bond pdb=" C4' G47 D 71 " pdb=" C3' G47 D 71 " ideal model delta sigma weight residual 1.303 1.513 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C4' G47 D 71 " pdb=" O4' G47 D 71 " ideal model delta sigma weight residual 1.623 1.450 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" N3 G47 D 71 " pdb=" C4 G47 D 71 " ideal model delta sigma weight residual 1.492 1.347 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C2 G47 D 71 " pdb=" N3 G47 D 71 " ideal model delta sigma weight residual 1.462 1.320 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C2 G47 D 71 " pdb=" N2 G47 D 71 " ideal model delta sigma weight residual 1.454 1.340 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 8901 not shown) Histogram of bond angle deviations from ideal: 59.75 - 74.63: 3 74.63 - 89.51: 0 89.51 - 104.39: 326 104.39 - 119.28: 7506 119.28 - 134.16: 4484 Bond angle restraints: 12319 Sorted by residual: angle pdb=" C1' G47 D 71 " pdb=" N9 G47 D 71 " pdb=" C8 G47 D 71 " ideal model delta sigma weight residual 104.99 129.57 -24.58 3.00e+00 1.11e-01 6.71e+01 angle pdb=" O1P G47 D 71 " pdb=" P G47 D 71 " pdb=" O2P G47 D 71 " ideal model delta sigma weight residual 109.47 119.01 -9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C ASP A 256 " pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 120.30 115.22 5.08 1.64e+00 3.72e-01 9.58e+00 angle pdb=" C5 G47 D 71 " pdb=" C4 G47 D 71 " pdb=" N3 G47 D 71 " ideal model delta sigma weight residual 120.01 129.07 -9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" C5 G47 D 71 " pdb=" C6 G47 D 71 " pdb=" O6 G47 D 71 " ideal model delta sigma weight residual 120.00 128.65 -8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 12314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.25: 4708 18.25 - 36.51: 416 36.51 - 54.76: 69 54.76 - 73.02: 17 73.02 - 91.27: 9 Dihedral angle restraints: 5219 sinusoidal: 2455 harmonic: 2764 Sorted by residual: dihedral pdb=" CB GLU A 224 " pdb=" CG GLU A 224 " pdb=" CD GLU A 224 " pdb=" OE1 GLU A 224 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 211 " pdb=" CD ARG B 211 " pdb=" NE ARG B 211 " pdb=" CZ ARG B 211 " ideal model delta sinusoidal sigma weight residual 90.00 134.04 -44.04 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB ARG A 78 " pdb=" CG ARG A 78 " pdb=" CD ARG A 78 " pdb=" NE ARG A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -2.07 -57.93 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1257 0.073 - 0.147: 127 0.147 - 0.220: 4 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA NVP A 602 " pdb=" CB NVP A 602 " pdb=" CC NVP A 602 " pdb=" N1 NVP A 602 " both_signs ideal model delta sigma weight residual True 2.04 -2.41 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP B 401 " pdb=" N TRP B 401 " pdb=" C TRP B 401 " pdb=" CB TRP B 401 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C4' G47 D 71 " pdb=" C5' G47 D 71 " pdb=" O4' G47 D 71 " pdb=" C3' G47 D 71 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1387 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.050 2.00e-02 2.50e+03 9.30e-02 2.81e+02 pdb=" N9 G47 D 71 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.046 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.063 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.017 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.045 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.045 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.088 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.138 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.080 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.029 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OE NVP A 602 " -0.024 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" C10 NVP A 602 " 0.021 2.00e-02 2.50e+03 pdb=" C7 NVP A 602 " -0.048 2.00e-02 2.50e+03 pdb=" C9 NVP A 602 " -0.030 2.00e-02 2.50e+03 pdb=" N8 NVP A 602 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 195 " 0.023 2.00e-02 2.50e+03 2.47e-02 1.82e+01 pdb=" N9 G C 195 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G C 195 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C 195 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G C 195 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G C 195 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 195 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G C 195 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 195 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 195 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G C 195 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G C 195 " 0.047 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 128 2.66 - 3.22: 7870 3.22 - 3.78: 13947 3.78 - 4.34: 19287 4.34 - 4.90: 31048 Nonbonded interactions: 72280 Sorted by model distance: nonbonded pdb=" OD2 ASP A 443 " pdb="MG MG A 601 " model vdw 2.100 2.170 nonbonded pdb=" O ASN A 474 " pdb=" OG1 THR A 477 " model vdw 2.206 2.440 nonbonded pdb=" NZ LYS B 323 " pdb=" OE2 GLU B 344 " model vdw 2.213 2.520 nonbonded pdb=" OE2 GLU A 79 " pdb=" NH2 ARG A 83 " model vdw 2.268 2.520 nonbonded pdb=" OG SER B 134 " pdb=" O THR B 139 " model vdw 2.282 2.440 ... (remaining 72275 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: 3.650 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: 13.040 Check model and map are aligned: 0.170 Set scattering table: 0.080 Process input model: 30.310 Find NCS groups from input model: 0.220 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 0.210 8906 Z= 0.309 Angle : 0.694 24.577 12319 Z= 0.353 Chirality : 0.044 0.367 1390 Planarity : 0.006 0.093 1383 Dihedral : 14.033 91.274 3435 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.94 (0.29), residues: 938 helix: 2.07 (0.32), residues: 317 sheet: -0.79 (0.42), residues: 161 loop : 0.25 (0.31), residues: 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.988 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2429 time to fit residues: 39.8024 Evaluate side-chains 85 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 39 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8906 Z= 0.179 Angle : 0.501 7.319 12319 Z= 0.245 Chirality : 0.040 0.152 1390 Planarity : 0.004 0.041 1383 Dihedral : 6.765 88.952 1525 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.94 (0.29), residues: 938 helix: 1.93 (0.31), residues: 317 sheet: -0.52 (0.41), residues: 170 loop : 0.26 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.019 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.2223 time to fit residues: 28.8212 Evaluate side-chains 82 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8906 Z= 0.317 Angle : 0.536 7.175 12319 Z= 0.264 Chirality : 0.041 0.140 1390 Planarity : 0.004 0.037 1383 Dihedral : 7.107 89.162 1525 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.11 % Allowed : 7.13 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.70 (0.28), residues: 938 helix: 1.53 (0.31), residues: 319 sheet: -0.49 (0.42), residues: 162 loop : 0.19 (0.30), residues: 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.013 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 97 average time/residue: 0.2200 time to fit residues: 30.0881 Evaluate side-chains 80 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0864 time to fit residues: 1.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8906 Z= 0.264 Angle : 0.504 7.105 12319 Z= 0.247 Chirality : 0.040 0.173 1390 Planarity : 0.004 0.034 1383 Dihedral : 7.195 89.331 1525 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.86 % Allowed : 9.34 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.63 (0.28), residues: 938 helix: 1.46 (0.30), residues: 322 sheet: -0.58 (0.41), residues: 159 loop : 0.16 (0.30), residues: 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.952 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 83 average time/residue: 0.2217 time to fit residues: 25.8144 Evaluate side-chains 81 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0950 time to fit residues: 1.8366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 278 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8906 Z= 0.200 Angle : 0.475 7.121 12319 Z= 0.232 Chirality : 0.039 0.150 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.182 88.846 1525 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.74 % Allowed : 11.06 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.79 (0.28), residues: 938 helix: 1.66 (0.30), residues: 321 sheet: -0.51 (0.40), residues: 159 loop : 0.21 (0.30), residues: 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.948 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 83 average time/residue: 0.2247 time to fit residues: 26.1028 Evaluate side-chains 77 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8906 Z= 0.190 Angle : 0.477 7.117 12319 Z= 0.231 Chirality : 0.039 0.140 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.182 88.705 1525 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.98 % Allowed : 11.06 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.85 (0.28), residues: 938 helix: 1.74 (0.30), residues: 321 sheet: -0.40 (0.40), residues: 159 loop : 0.20 (0.30), residues: 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 2.146 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 82 average time/residue: 0.2998 time to fit residues: 33.9108 Evaluate side-chains 78 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0932 time to fit residues: 1.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 0.0070 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8906 Z= 0.194 Angle : 0.480 7.152 12319 Z= 0.232 Chirality : 0.039 0.140 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.196 88.613 1525 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.25 % Allowed : 11.67 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.82 (0.28), residues: 938 helix: 1.71 (0.30), residues: 321 sheet: -0.32 (0.40), residues: 161 loop : 0.14 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.042 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.2316 time to fit residues: 25.1209 Evaluate side-chains 72 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8906 Z= 0.241 Angle : 0.495 7.173 12319 Z= 0.240 Chirality : 0.039 0.139 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.239 88.718 1525 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.37 % Allowed : 12.41 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.74 (0.28), residues: 938 helix: 1.60 (0.30), residues: 322 sheet: -0.35 (0.40), residues: 161 loop : 0.12 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.979 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.2445 time to fit residues: 25.8092 Evaluate side-chains 76 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1130 time to fit residues: 1.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 197 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8906 Z= 0.252 Angle : 0.499 7.139 12319 Z= 0.243 Chirality : 0.040 0.142 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.284 88.907 1525 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.12 % Allowed : 12.90 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.70 (0.28), residues: 938 helix: 1.56 (0.30), residues: 322 sheet: -0.39 (0.40), residues: 161 loop : 0.11 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.892 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2382 time to fit residues: 24.4030 Evaluate side-chains 73 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0770 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 269 GLN A 373 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8906 Z= 0.169 Angle : 0.466 7.113 12319 Z= 0.226 Chirality : 0.039 0.139 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.218 88.548 1525 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.12 % Allowed : 13.39 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.84 (0.28), residues: 938 helix: 1.71 (0.30), residues: 321 sheet: -0.28 (0.39), residues: 161 loop : 0.14 (0.29), residues: 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.997 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.2432 time to fit residues: 26.4155 Evaluate side-chains 75 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0749 time to fit residues: 1.3110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.168783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125539 restraints weight = 9260.336| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.60 r_work: 0.3324 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8906 Z= 0.175 Angle : 0.470 7.123 12319 Z= 0.227 Chirality : 0.039 0.136 1390 Planarity : 0.004 0.035 1383 Dihedral : 7.188 88.397 1525 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.12 % Allowed : 13.02 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.85 (0.28), residues: 938 helix: 1.68 (0.30), residues: 321 sheet: -0.24 (0.40), residues: 161 loop : 0.17 (0.30), residues: 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.87 seconds wall clock time: 38 minutes 7.35 seconds (2287.35 seconds total)